Citrus Sinensis ID: 024786

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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-------260--
Protein Sequence
MPTDSNENNNNNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPDLAISTPGNGLK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccHHHHcccccccccccccccccccccEEEEEcccccccccHHHccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccHHHcccccccccccccccccccccEEEEEcccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccEEEccccccc
Coil and Loop (DISEMBL)
mptdsnennnnnnnnssssssnkrvtaknpaaeqeqlpcprcestntkfcyynnynfsqprhfckscrrywthggtlrdipvgggtrknakrcrtipsstcaatntmsitpgvavgsahqdyplhatpvlvpfqggsaplkaanmnggygvcgngtgaggfasllspqgpgflalggfglglgsgfvgdvglaglgrgawglagvsdagaaaanggggggssgigntwqfesgeatttsgfgtadcfswpdlaistpgnglk
Flexible Loop (DISEMBL)
mptdsnennnnnnnnssssssnkRVTAKnpaaeqeqlpcprceSTNTKFCYYNNYNFSQPRHFCKSCRRYWTHggtlrdipvgggtrknakrcrtipsstcaatntMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFswpdlaistpgnglk
Low Complexity Region (SEG)
MPTDsnennnnnnnnssssssnKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNggygvcgngtgaggFASLLSPQgpgflalggfglglgsgfvgdvglaglgrgawglagvsdagaaaanggggggssgigNTWQFESGEATTTSGFGTADCFSWPDLAISTPGNGLK
Disordered region (IsUnstruct)
*****************************************CESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGV*********************************************************
Disordered Region (DISOPRED)
****************************************RCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRD****************************************************************************************************************************************************************GFGTADCFSWPDLAISTPG****
Disordered Region (DISEMBL)
*************************************PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPDLAI********
Disordered Region (DISPRO)
**********************************EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVG***************************************PLHATPVLVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPDLAISTPGN***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPTDSNENNNNNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPDLAISTPGNGLK
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	262	2.2.26 [Sep-21-2011]
Q39088	253	Dof zinc finger protein D	yes	no	0.843	0.873	0.451	3e-42
Q9FGD6	225	Dof zinc finger protein D	no	no	0.713	0.831	0.462	4e-39
O82155	194	Dof zinc finger protein D	no	no	0.255	0.345	0.791	3e-27
Q84TE9	257	Dof zinc finger protein D	no	no	0.606	0.618	0.401	1e-24
Q8LDR0	307	Dof zinc finger protein D	no	no	0.312	0.267	0.623	2e-24
Q9M1E6	245	Dof zinc finger protein D	no	no	0.354	0.379	0.495	3e-24
O24463	328	Dof zinc finger protein P	N/A	no	0.236	0.189	0.709	4e-24
Q9LSL6	316	Dof zinc finger protein D	no	no	0.297	0.246	0.602	6e-24
O80928	330	Dof zinc finger protein D	no	no	0.259	0.206	0.647	2e-23
Q8LFV3	448	Cyclic dof factor 3 OS=Ar	no	no	0.461	0.270	0.435	2e-23

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

 Score =  172 bits (435), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 107/237 (45%), Positives = 135/237 (56%), Gaps = 16/237 (6%)

Query: 33  EQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKR 92
           +QEQLPCPRC+S+NTKFCYYNNYNFSQPRHFCK+CRRYWTHGGTLRD+PVGGGTRK+AKR
Sbjct: 26  QQEQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKACRRYWTHGGTLRDVPVGGGTRKSAKR 85

Query: 93  CRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVP----FQGGSAPLKAANMNG- 147
            R     TC+ +++ S      V S     PL  TPVL P      G +  +  ++  G 
Sbjct: 86  SR-----TCSNSSSSS---VSGVVSNSNGVPLQTTPVLFPQSSISNGVTHTVTESDGKGS 137

Query: 148 GYGVCGNGTGA--GGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGV 205
              +CG+ T       A+  +  G G +   G           DV   GLGR  W  + V
Sbjct: 138 ALSLCGSFTSTLLNHNAAATATHGSGSVIGIGGFGIGLGSGFDDVSF-GLGRAMWPFSTV 196

Query: 206 SDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPDLAISTPGNGLK 262
             A        GG  +  +  TWQFE  E+    GF + + F+WPDL+I+TPGN LK
Sbjct: 197 GTATTTNVGSNGGHHAVPMPATWQFEGLESNAGGGFVSGEYFAWPDLSITTPGNSLK 253

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 =  161 bits (407), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 105/227 (46%), Positives = 128/227 (56%), Gaps = 40/227 (17%)

Query: 30  PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN 89
           P  +QEQL CPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGG +RK+
Sbjct: 25  PTDQQEQLSCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGVSRKS 84

Query: 90  AKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGY 149
           +KR RT  S   AAT ++       VGS  +++PL ATPVL P          ++ NGG 
Sbjct: 85  SKRSRTYSS---AATTSV-------VGS--RNFPLQATPVLFP---------QSSSNGGI 123

Query: 150 GVCGNGTGA--GGFASLLSPQGP--------GFLALGGFGLGLGSGFVGDVGLAGLGRGA 199
                   +  GGF+SL++            GF     FGLGLG G   +    G G   
Sbjct: 124 TTAKGSASSFYGGFSSLINYNAAVSRNGPGGGFNGPDAFGLGLGHGSYYEDVRYGQGITV 183

Query: 200 WGL-AGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTAD 245
           W   +G +DA    ++       + I  TWQFE  E+    GF + D
Sbjct: 184 WPFSSGATDAATTTSH------IAQIPATWQFEGQESKV--GFVSGD 222

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 = 53/67 (79%), Positives = 58/67 (86%)

Query: 33 EQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKR 92
          EQEQL CPRC+S NTKFCYYNNYN SQPRHFCK+CRRYWT GG LR+IPVGGGTRK+ KR
Sbjct: 29 EQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGALRNIPVGGGTRKSNKR 88

Query: 93 CRTIPSS 99
            + PSS
Sbjct: 89 SGSSPSS 95

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 =  113 bits (282), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 79/197 (40%), Positives = 97/197 (49%), Gaps = 38/197 (19%)

Query: 30  PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN 89
           P   +  L CPRC+STNTKFCYYNNY+ +QPR+FCKSCRRYWT GGTLR+IPVGGG RKN
Sbjct: 48  PQPPELALRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPVGGGCRKN 107

Query: 90  AKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGY 149
            +       ST +A  ++  TP                    P         AA  N GY
Sbjct: 108 KR-------STSSAARSLRTTPE-------------------PASHDGKVFSAAGFN-GY 140

Query: 150 GVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAG 209
               +   +  FA LL+ Q PG  +  GF   LGS    D+          G+ G S   
Sbjct: 141 SNNEHIDLSLAFA-LLNKQHPGSSSQLGFHSELGSSHQSDME---------GMFGTSQQK 190

Query: 210 AAAANGGGGGGSSGIGN 226
             A     G GSSG+G+
Sbjct: 191 ENATY-AFGNGSSGLGD 206

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 =  113 bits (282), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/85 (62%), Positives = 60/85 (70%), Gaps = 3/85 (3%)

Query: 24  RVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVG 83
           R    N     + L CPRC S NTKFCYYNNYN SQPRHFCK+CRRYWT GG LR++PVG
Sbjct: 38  RAHQNNILNHHQSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVG 97

Query: 84  GGTRKNAKRCRT--IPSSTCAATNT 106
           GG RK AKR +T  +PSS+ A   T
Sbjct: 98  GGCRK-AKRSKTKQVPSSSSADKPT 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|Q9M1E6|DOF32_ARATH Dof zinc finger protein DOF3.2 OS=Arabidopsis thaliana GN=DOF3.2 PE=2 SV=1

 Score =  112 bits (280), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 50/101 (49%), Positives = 68/101 (67%), Gaps = 8/101 (7%)

Query: 23  KRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPV 82
           K ++A  PA  ++ L CPRC+STNTKFCYYNNY+ SQPR+FCKSCRRYWT GG LR+IP+
Sbjct: 26  KPLSATRPAPPEQSLRCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGILRNIPI 85

Query: 83  GGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYP 123
           GG  RK+ +        + +AT ++  TP   +    + +P
Sbjct: 86  GGAYRKHKR--------SSSATKSLRTTPEPTMTHDGKSFP 118

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

Arabidopsis thaliana (taxid: 3702)

>sp|O24463|PBF_MAIZE Dof zinc finger protein PBF OS=Zea mays GN=PBF PE=1 SV=1

 Score =  111 bits (278), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 52/62 (83%)

Query: 35  EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCR 94
           E L CPRC+S NTKFCYYNNY+ SQPR+FCK+CRRYWTHGGTLR++P+GGG RKN    R
Sbjct: 58  EALKCPRCDSNNTKFCYYNNYSMSQPRYFCKACRRYWTHGGTLRNVPIGGGCRKNKHASR 117

Query: 95  TI 96
            +
Sbjct: 118 FV 119

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

 Score =  111 bits (277), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 47/78 (60%), Positives = 58/78 (74%)

Query: 17 SSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGT 76
          S +S  K+  + + A +Q+ L CPRC S NTKFCYYNNY+ SQPRHFCKSCRRYWT GG 
Sbjct: 21 SGTSQTKKPPSSSVAQDQQNLKCPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGA 80

Query: 77 LRDIPVGGGTRKNAKRCR 94
          LR++P+GGG RK  K  +
Sbjct: 81 LRNVPIGGGCRKTKKSIK 98

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

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 =  109 bits (272), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 44/68 (64%), Positives = 53/68 (77%)

Query: 24  RVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVG 83
           R    N A  +  L CPRCESTNTKFCY+NNY+ +QPRHFCK+CRRYWT GG LR++PVG
Sbjct: 76  RARQANVALPEAALKCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVG 135

Query: 84  GGTRKNAK 91
           GG R+N +
Sbjct: 136 GGCRRNRR 143

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (272), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 61/140 (43%), Positives = 81/140 (57%), Gaps = 19/140 (13%)

Query: 3   TDSNENNNNNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRH 62
           TD  E+++   +N  ++   K  T K P    + LPCPRC+S  TKFCYYNNYN +QPRH
Sbjct: 81  TDQIESSDTPEDNQQTTPDGK--TLKKPT---KILPCPRCKSMETKFCYYNNYNINQPRH 135

Query: 63  FCKSCRRYWTHGGTLRDIPVGGGTRKNAK-----RCRTIPSSTCAA-------TNTMSIT 110
           FCK+C+RYWT GGT+R++PVG G RKN       R  TI  +  AA        NT  ++
Sbjct: 136 FCKACQRYWTAGGTMRNVPVGAGRRKNKSSSSHYRHITISEALEAARLDPGLQANTRVLS 195

Query: 111 PGVAVGSAHQDYPLHATPVL 130
            G+     H   P+  TPV+
Sbjct: 196 FGLEAQQQHVAAPM--TPVM 213

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	262
224096854	248	predicted protein [Populus trichocarpa]	0.835	0.883	0.602	2e-62
224081531	253	predicted protein [Populus trichocarpa]	0.946	0.980	0.558	1e-56
356498503	234	PREDICTED: dof zinc finger protein DOF3.	0.847	0.948	0.521	3e-52
255562705	245	zinc finger protein, putative [Ricinus c	0.881	0.942	0.5	2e-50
225458485	226	PREDICTED: dof zinc finger protein DOF3.	0.832	0.964	0.513	2e-47
359480417	220	PREDICTED: dof zinc finger protein DOF3.	0.805	0.959	0.527	1e-45
356559454	236	PREDICTED: dof zinc finger protein DOF3.	0.877	0.974	0.468	4e-45
37051131	234	DNA binding with one finger 5 protein [P	0.858	0.961	0.482	1e-44
388491986	229	unknown [Medicago truncatula]	0.851	0.973	0.460	2e-44
449448364	239	PREDICTED: dof zinc finger protein DOF3.	0.816	0.895	0.527	3e-42

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

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 141/234 (60%), Positives = 159/234 (67%), Gaps = 15/234 (6%)

Query: 30  PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN 89
           P  EQE LPCPRC+STNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN
Sbjct: 29  PPQEQEHLPCPRCDSTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN 88

Query: 90  AKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGY 149
           AKR RT      +AT+  S   G   G+     PL ATPVL+P         + +  GG 
Sbjct: 89  AKRSRT------SATSPASFM-GPMTGTNIDGLPLPATPVLLPLTANQG--LSVHFGGGD 139

Query: 150 GVCGNGTGAGGFASLLSPQGP-GFLALGGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDA 208
           G    G   G F SLL+ QGP GFLAL GFGLG+G G + DV  A LGRG W   G+ D 
Sbjct: 140 GKGNGGGLGGSFTSLLNTQGPAGFLALNGFGLGIGPG-IEDVNFA-LGRGLWPFPGMGDV 197

Query: 209 GAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPDLAISTPGNGLK 262
           GA+    GG   ++G+GNTWQFE+G+    +GF   DCFSWPDLAISTPGNGLK
Sbjct: 198 GASVGGNGGAAVTAGLGNTWQFENGQE---NGFVGGDCFSWPDLAISTPGNGLK 248

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

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 =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 149/267 (55%), Positives = 171/267 (64%), Gaps = 19/267 (7%)

Query: 1   MPTD-SNENNNNNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQ 59
           MPT+ S+         S++ +SNK   A  P  EQE LPCPRC+STNTKFCYYNNYNFSQ
Sbjct: 1   MPTELSSSEKTRRPPLSTTPTSNKPGGA--PPQEQEHLPCPRCDSTNTKFCYYNNYNFSQ 58

Query: 60  PRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAH 119
           PRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKR RT  S+T AA+       G  + +  
Sbjct: 59  PRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRSRT--SATTAASFA-----GPIIDNNI 111

Query: 120 QDYPLHATPVLVPF---QGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGP-GFLAL 175
            + PL ATPVLVP    QG S      +   G G CG+G   G F SLL+  GP G LAL
Sbjct: 112 DNLPLPATPVLVPLTASQGFSVHFGGGSDGKGNGGCGSGALGGSFTSLLNTPGPAGILAL 171

Query: 176 GGFGLGLGSGFVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEA 235
           G FG GLG G + DVG  GLGRG W   G+ D+GA     GG   ++G+ NTWQF S   
Sbjct: 172 GRFGHGLGHG-LEDVG-CGLGRGLWSFPGIGDSGAGVGGHGGVTVTAGLDNTWQFGSAGQ 229

Query: 236 TTTSGFGTADCFSWPDLAISTPGNGLK 262
              +GF   DCFSWP+LAISTP NG K
Sbjct: 230 ---NGFVGGDCFSWPELAISTPANGFK 253

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  211 bits (536), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 134/257 (52%), Positives = 157/257 (61%), Gaps = 35/257 (13%)

Query: 16  SSSSSSNKRVT-------AKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCR 68
           SS+S  ++R +       A  P  EQE LPCPRC+STNTKFCYYNNYN+SQPRHFCKSCR
Sbjct: 3   SSNSGESRRASKPQSSGGAAPPPPEQENLPCPRCDSTNTKFCYYNNYNYSQPRHFCKSCR 62

Query: 69  RYWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATP 128
           RYWTHGGTLRDIPVGGG+RKNAKR RT            S +   +  ++ Q++  HA  
Sbjct: 63  RYWTHGGTLRDIPVGGGSRKNAKRSRT------HHVAATSSSSTSSTMTSAQEH--HAHT 114

Query: 129 VLVPFQGGSAPLKAANMNGGYGVCGNGTG--AGGFASLL-SPQGPGFLALGGFGLGLGSG 185
           +L P     A      ++G      NG G   G F SLL +  G GFLALGGFGLG G  
Sbjct: 115 LLAPV----ASTHYGVLDGDVKQTSNGNGNVCGSFTSLLNNTHGSGFLALGGFGLGHG-- 168

Query: 186 FVGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTAD 245
              D+G  G+GR  W   G+ D G    N GG   SSG+ NTWQ ESGE     GF + D
Sbjct: 169 -YDDMGF-GIGRSGWAFPGMVDGG----NIGGAVASSGL-NTWQLESGEG----GFVSGD 217

Query: 246 CFSWPDLAISTPGNGLK 262
           CF+WP LAISTPGNGLK
Sbjct: 218 CFAWPGLAISTPGNGLK 234

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562705|ref|XP_002522358.1| zinc finger protein, putative [Ricinus communis] gi|223538436|gb|EEF40042.1| zinc finger protein, putative [Ricinus communis]

 Score =  205 bits (521), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 129/258 (50%), Positives = 145/258 (56%), Gaps = 27/258 (10%)

Query: 16  SSSSSSNKRVTAKN------PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR 69
            + S+  KR+T  +      P  E E LPCPRC+STNTKFCYYNNYNFSQPRHFCKSCRR
Sbjct: 4   DTCSTETKRLTKPHNNVPGAPPPEHEHLPCPRCDSTNTKFCYYNNYNFSQPRHFCKSCRR 63

Query: 70  YWTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPV 129
           YWTHGGTLRDIP+GGGTRKNAKR RT          + ++   +       + PL ATPV
Sbjct: 64  YWTHGGTLRDIPIGGGTRKNAKRSRT----------SSAVVGPITSNPVDHNLPLSATPV 113

Query: 130 LVPFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGD 189
           LVP             NG      N T  G F SLL+ QGPG     G           D
Sbjct: 114 LVPLMANQGQFIDGKGNGN-NTTANSTVCGSFTSLLNTQGPG-FLALGGFGLGLGTGFED 171

Query: 190 VGLAGLGRGAWGLAGV----SDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGF-GTA 244
           VG  GLGRG W   GV    +  G       GGG  +G+ NTW FE G     +GF G  
Sbjct: 172 VGF-GLGRGVWPFPGVGDGGASLGGGHGGSVGGGAVTGMSNTWHFEGGAE---NGFVGAG 227

Query: 245 DCFSWPDLAISTPGNGLK 262
           DCFSWPDLAISTPGNGLK
Sbjct: 228 DCFSWPDLAISTPGNGLK 245

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  194 bits (494), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 129/251 (51%), Positives = 146/251 (58%), Gaps = 33/251 (13%)

Query: 18  SSSSNKRVTAKNPA----AEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTH 73
           S S  +RV           + E LPCPRC+STNTKFCYYNNYN SQPRHFCKSCRRYWT 
Sbjct: 3   SESGERRVARPQQVGGHPPQSEHLPCPRCDSTNTKFCYYNNYNLSQPRHFCKSCRRYWTQ 62

Query: 74  GGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPF 133
           GGTLR+IPVGGGTRKN+KR RT  SS+ +   T                P+  +PVL   
Sbjct: 63  GGTLRNIPVGGGTRKNSKRSRTATSSSSSTLETTPAN------------PISVSPVL--- 107

Query: 134 QGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGLA 193
               A  +    N   G+  NG  +GGF SLL+ QGPGFLAL GF LGLG GF  ++G  
Sbjct: 108 ---KAETETPQRN---GLSLNGDVSGGFTSLLNSQGPGFLALNGFSLGLGPGF-DEMGF- 159

Query: 194 GLGRGAWGLAGVSDA--GAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWPD 251
           G  +G W    V D   G      GGG  SS I NTWQ   GE     GF   DCF+WPD
Sbjct: 160 GPAKGVWSYPDVGDVVLGGDGTGSGGGSASSSICNTWQLSGGEV----GFVDGDCFAWPD 215

Query: 252 LAISTPGNGLK 262
           LAISTPG GLK
Sbjct: 216 LAISTPGQGLK 226

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480417|ref|XP_003632455.1| PREDICTED: dof zinc finger protein DOF3.4-like [Vitis vinifera] gi|147810110|emb|CAN75830.1| hypothetical protein VITISV_039634 [Vitis vinifera]

 Score =  189 bits (479), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 133/252 (52%), Positives = 147/252 (58%), Gaps = 41/252 (16%)

Query: 18  SSSSNKRVTAKN----PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTH 73
           S S +KR +  +    P  EQE LPCPRC+STNTKFCYYNNYNFSQPRHFCKSCRRYWTH
Sbjct: 3   SDSGDKRPSKPHQTGAPPPEQEHLPCPRCDSTNTKFCYYNNYNFSQPRHFCKSCRRYWTH 62

Query: 74  GGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPF 133
           GGTLRDIPVGGG+RKNAKR RT                     SA    PL ATPVLV  
Sbjct: 63  GGTLRDIPVGGGSRKNAKRSRT------------------TTSSASSQEPLPATPVLVSL 104

Query: 134 ---QGGSAPLKAANMNGGYGVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDV 190
                 S P    ++     VCG+      F SLL+ QGPG     G           D+
Sbjct: 105 STNHATSMPF-VGDVKPTVNVCGS------FTSLLNTQGPG-FLALGGFGLGLGPGFEDM 156

Query: 191 GLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWP 250
           G  GLGRG W   G  D GA+      GGG++ +GNTWQFESGE     GF   DCFSWP
Sbjct: 157 GF-GLGRGVWPFPGAGDGGASGGT---GGGTALVGNTWQFESGEG----GFVAGDCFSWP 208

Query: 251 DLAISTPGNGLK 262
           DLAISTPGNGLK
Sbjct: 209 DLAISTPGNGLK 220

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  187 bits (475), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 141/252 (55%), Gaps = 22/252 (8%)

Query: 13  NNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWT 72
           N+  S  +S    +   P  E E LPCPRC+S NTKFCYYNNYN+SQPRHFCKSCRRYWT
Sbjct: 5   NSGESRRASKPHRSVAAPPVEPENLPCPRCDSANTKFCYYNNYNYSQPRHFCKSCRRYWT 64

Query: 73  HGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVP 132
           HGGTLRDIPVGGG+RKNAKR RT  ++   ++++ + +   +    H  + L A      
Sbjct: 65  HGGTLRDIPVGGGSRKNAKRSRTHHAAAATSSSSSTSSATTSAHEHHNAHTLTAL----- 119

Query: 133 FQGGSAPLKAANMNGGYGVCG--NGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDV 190
                AP+ AA   G  G     NG   G + SLL+          G           D+
Sbjct: 120 -----APVTAATHFGHDGDVKQTNGNACGSYTSLLNNTQGSGFFALGGFGLGLGHGFDDM 174

Query: 191 GLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSWP 250
           G  G+GR  W   G+ D G    N GG   SSG+ NTWQ ESGE     GF   DCFSWP
Sbjct: 175 GF-GIGRSGWAFPGMVDNG----NIGGAIASSGV-NTWQLESGEG----GFVGGDCFSWP 224

Query: 251 DLAISTPGNGLK 262
            LAISTPGNGLK
Sbjct: 225 GLAISTPGNGLK 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|37051131|dbj|BAC81662.1| DNA binding with one finger 5 protein [Pisum sativum]

 Score =  185 bits (470), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 122/253 (48%), Positives = 147/253 (58%), Gaps = 28/253 (11%)

Query: 16  SSSSSSNKRVTAKN----PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYW 71
           S S  S + +  +N    PA EQE LPCPRC+STNTKFCYYNNYN+SQPRH CK+CRRYW
Sbjct: 4   SDSGESRRSIKPQNRPGAPAPEQENLPCPRCDSTNTKFCYYNNYNYSQPRHLCKACRRYW 63

Query: 72  THGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLV 131
           THGGTLRDIPVGGGTRKNAKR RT   +  +++++ +        +  Q+Y     P + 
Sbjct: 64  THGGTLRDIPVGGGTRKNAKRSRTHHVAVTSSSSSSA-----VTSAPEQNY-----PSMT 113

Query: 132 PFQGGSAPLKAANMNGGYGVCGNGTGAGGFASLL--SPQGPGFLALGGFGLGLGSGFVGD 189
           P QGGS P    +  G      N +  G F SLL  +PQ        G         +GD
Sbjct: 114 PIQGGSFPYGGVDGEGKQ----NMSVCGSFTSLLNNNPQQNSGFLALGGFGLGLGHGLGD 169

Query: 190 VGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADCFSW 249
           +G  G+GR  W   G+ D     +N G    SSGIGN+WQ E GE       G  DCFSW
Sbjct: 170 MGF-GIGR-EWSFPGMMD----GSNMGVPVVSSGIGNSWQLEGGETGFVG--GGGDCFSW 221

Query: 250 PDLAISTPGNGLK 262
           P LAISTPGNGLK
Sbjct: 222 PGLAISTPGNGLK 234

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491986|gb|AFK34059.1| unknown [Medicago truncatula]

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 118/256 (46%), Positives = 144/256 (56%), Gaps = 33/256 (12%)

Query: 11  NNNNNSSSSSSNKRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRY 70
           ++++  S  S+  ++    PA EQE LPCPRC+STNTKFCYYNNYN+SQPRHFCK+CRRY
Sbjct: 3   SSDSGESRRSTKPQIRPGAPAPEQENLPCPRCDSTNTKFCYYNNYNYSQPRHFCKACRRY 62

Query: 71  WTHGGTLRDIPVGGGTRKNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVL 130
           WTHGGTLRDIPVGGGTRKNAKR R         TN +++T   AV SA  +Y  H    +
Sbjct: 63  WTHGGTLRDIPVGGGTRKNAKRSR---------TNHVAVTSSSAVTSAAPEY--HHYQTI 111

Query: 131 VPFQGGSAPLKAANMNGGYGVCGNG----TGAGGFASLLSPQGPGFLALGGFGLGLGSGF 186
              QGGS P          GV G+G    +  G F SLL+       + G   LG     
Sbjct: 112 SAVQGGSFPFSG-------GVDGDGKQNMSVCGSFTSLLNNNNNNNQSSGFLALGGFGLG 164

Query: 187 VGDVGLAGLGRGAWGLAGVSDAGAAAANGGGGGGSSGIGNTWQFESGEATTTSGFGTADC 246
           + ++G  G+GR  W   G+ D     +          +GNTWQ E GE          DC
Sbjct: 165 LEEMGF-GIGRTGWAFPGMMDGVPVVS-------PGVVGNTWQLEGGEGGFVG---AGDC 213

Query: 247 FSWPDLAISTPGNGLK 262
           FSWP LAISTP NGLK
Sbjct: 214 FSWPGLAISTPVNGLK 229

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448364|ref|XP_004141936.1| PREDICTED: dof zinc finger protein DOF3.4-like [Cucumis sativus]

 Score =  177 bits (450), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 124/235 (52%), Positives = 142/235 (60%), Gaps = 21/235 (8%)

Query: 30  PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN 89
           P  EQE LPCPRC+STNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGG+RKN
Sbjct: 24  PPPEQEHLPCPRCDSTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGSRKN 83

Query: 90  AKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAANMNGGY 149
           AKR RT   ++ A  ++ S        S    +PL ATPVL         +      GG 
Sbjct: 84  AKRSRTCIPTSAAIVSSSSSGSFSNSVSRLDHHPLPATPVL---VPLGGGVGGDLKVGGG 140

Query: 150 GVCGNGTGAGGFASLLSPQGPGFLALGGFGLGLGSGFVGDVGL-AGLGRGAWGLAGVSDA 208
            +CG+      F SLL+   PGF +LGG           DVG      R AW   G+ D 
Sbjct: 141 NMCGS------FTSLLNTHAPGFWSLGG-FGLGLGSGFEDVGYGTASSRVAWPFLGLGDG 193

Query: 209 GAAAANGGGGGGSSGIGNTWQFESGEATTTSGF-GTADCFSWPDLAISTPGNGLK 262
           GA         G  G  NTWQFE+G+A   +GF G+ADC SWP+LAISTPGNGLK
Sbjct: 194 GAGVG------GHGGTPNTWQFENGDA---AGFVGSADCLSWPELAISTPGNGLK 239

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	262
TAIR|locus:2074850	253	OBP1 "OBF binding protein 1" [	0.351	0.363	0.68	8.6e-45
TAIR|locus:2158078	225	AT5G66940 [Arabidopsis thalian	0.389	0.453	0.640	1.7e-36
TAIR|locus:505006172	209	AT1G47655 [Arabidopsis thalian	0.320	0.401	0.593	5.3e-30
TAIR|locus:2094746	204	DOF2 "DOF zinc finger protein	0.293	0.377	0.701	3.9e-28
TAIR|locus:2017567	194	DOF1 "DOF zinc finger protein	0.255	0.345	0.791	1.3e-27
TAIR|locus:2039959	369	DAG2 "DOF AFFECTING GERMINATIO	0.320	0.227	0.6	2.8e-27
TAIR|locus:2032153	325	AT1G28310 [Arabidopsis thalian	0.351	0.283	0.559	9.4e-27
TAIR|locus:2026595	339	OBP2 [Arabidopsis thaliana (ta	0.419	0.324	0.465	1.9e-26
TAIR|locus:2159275	307	OBP4 "OBF binding protein 4" [	0.297	0.254	0.641	3.6e-25
TAIR|locus:2155755	316	AT5G65590 [Arabidopsis thalian	0.297	0.246	0.583	9.7e-25

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

 Score = 372 (136.0 bits), Expect = 8.6e-45, Sum P(2) = 8.6e-45
 Identities = 68/100 (68%), Positives = 80/100 (80%)

Query:    33 EQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKR 92
             +QEQLPCPRC+S+NTKFCYYNNYNFSQPRHFCK+CRRYWTHGGTLRD+PVGGGTRK+AKR
Sbjct:    26 QQEQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKACRRYWTHGGTLRDVPVGGGTRKSAKR 85

Query:    93 CRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVP 132
              RT     C+ +++ S++ GV   S     PL  TPVL P
Sbjct:    86 SRT-----CSNSSSSSVS-GVVSNS--NGVPLQTTPVLFP 117

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

 Score = 369 (135.0 bits), Expect = 1.7e-36, Sum P(2) = 1.7e-36
 Identities = 73/114 (64%), Positives = 84/114 (73%)

Query:    30 PAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKN 89
             P  +QEQL CPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGG +RK+
Sbjct:    25 PTDQQEQLSCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGVSRKS 84

Query:    90 AKRCRTIPSSTCAATNTMSITPGVAVGSAHQDYPLHATPVLVPFQGGSAPLKAA 143
             +KR RT  S   AAT ++       VGS  +++PL ATPVL P    +  +  A
Sbjct:    85 SKRSRTYSS---AATTSV-------VGS--RNFPLQATPVLFPQSSSNGGITTA 126

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

 Score = 295 (108.9 bits), Expect = 5.3e-30, Sum P(2) = 5.3e-30
 Identities = 51/86 (59%), Positives = 67/86 (77%)

Query:    26 TAKNPAAE-QEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGG 84
             TA  P     E LPCPRC ST TKFCYYNNYN +QPR++CKSCRRYWT GGTLRD+PVGG
Sbjct:    17 TAAYPPPNLAEPLPCPRCNSTTTKFCYYNNYNLAQPRYYCKSCRRYWTQGGTLRDVPVGG 76

Query:    85 GTRKNA-KRCRTIPSSTCAATNTMSI 109
             GTR+++ KR R+  ++  +++++ S+
Sbjct:    77 GTRRSSSKRHRSFSTTATSSSSSSSV 102

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 54/77 (70%), Positives = 63/77 (81%)

Query:    32 AEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAK 91
             AEQEQL CPRC+S NTKFCYYNNYN SQPRHFCKSCRRYWT GG LR++PVGGG+RKNA 
Sbjct:    24 AEQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALRNVPVGGGSRKNAT 83

Query:    92 RCRTIPSSTCAATNTMS 108
             +  T  SS+ ++ +  S
Sbjct:    84 KRSTSSSSSASSPSNSS 100

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

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 53/67 (79%), Positives = 58/67 (86%)

Query:    33 EQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKR 92
             EQEQL CPRC+S NTKFCYYNNYN SQPRHFCK+CRRYWT GG LR+IPVGGGTRK+ KR
Sbjct:    29 EQEQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGALRNIPVGGGTRKSNKR 88

Query:    93 CRTIPSS 99
               + PSS
Sbjct:    89 SGSSPSS 95

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

 Score = 283 (104.7 bits), Expect = 2.8e-27, Sum P(2) = 2.8e-27
 Identities = 51/85 (60%), Positives = 62/85 (72%)

Query:    25 VTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGG 84
             V A+  A  QE+L CPRC STNTKFCYYNNY+ +QPR+FCK CRRYWT GG+LR++PVGG
Sbjct:    68 VVAERKARPQEKLNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGG 127

Query:    85 GTRKNAKRCRTIPSSTCAATNTMSI 109
              +RKN KR  +  SS    T   S+
Sbjct:   128 SSRKN-KRSSSSSSSNILQTIPSSL 151

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:2032153 AT1G28310 [Arabidopsis thaliana (taxid:3702)]

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 52/93 (55%), Positives = 67/93 (72%)

Query:    28 KNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTR 87
             + P   Q QL CPRC+S+NTKFCYYNNY+ SQPRHFCK+C+RYWT GGTLR++PVGG  R
Sbjct:    32 QQPQQPQPQLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGSYR 91

Query:    88 KNAKRCRTIPSSTCAATNTMSITPGVAVGSAHQ 120
             KN KR +   ++T    +T+S T   +  + HQ
Sbjct:    92 KN-KRVKRPSTATTTTASTVSTTNSSSPNNPHQ 123

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 = 278 (102.9 bits), Expect = 1.9e-26, Sum P(2) = 1.9e-26
 Identities = 54/116 (46%), Positives = 72/116 (62%)

Query:    37 LPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCRT- 95
             L CPRC+S+NTKFCYYNNYN +QPRHFCK CRRYWT GG LR++PVGGG R+N K+ +  
Sbjct:    85 LKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRNNKKGKNG 144

Query:    96 -IPSSTCAATNTMSI---TPGVAVGSAHQDYPLHATPVLVPFQGG-SAPLKAANMN 146
              + SS+ ++  + S+   +P       +  +P   T   +   GG    L A N N
Sbjct:   145 NLKSSSSSSKQSSSVNAQSPSSGQLRTNHQFPFSPTLYNLTQLGGIGLNLAATNGN 200

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

 Score = 286 (105.7 bits), Expect = 3.6e-25, P = 3.6e-25
 Identities = 52/81 (64%), Positives = 59/81 (72%)

Query:    24 RVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVG 83
             R    N     + L CPRC S NTKFCYYNNYN SQPRHFCK+CRRYWT GG LR++PVG
Sbjct:    38 RAHQNNILNHHQSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVG 97

Query:    84 GGTRKNAKRCRT--IPSSTCA 102
             GG RK AKR +T  +PSS+ A
Sbjct:    98 GGCRK-AKRSKTKQVPSSSSA 117

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:2155755 AT5G65590 [Arabidopsis thaliana (taxid:3702)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 49/84 (58%), Positives = 61/84 (72%)

Query:    23 KRVTAKNPAAEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPV 82
             K+  + + A +Q+ L CPRC S NTKFCYYNNY+ SQPRHFCKSCRRYWT GG LR++P+
Sbjct:    27 KKPPSSSVAQDQQNLKCPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGALRNVPI 86

Query:    83 GGGTRKNAKRCR------TIPSST 100
             GGG RK  K  +      T+PSS+
Sbjct:    87 GGGCRKTKKSIKPNSSMNTLPSSS 110

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q39088	DOF34_ARATH	No assigned EC number	0.4514	0.8435	0.8735	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	262
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	1e-36
pfam03209	402	pfam03209, PUCC, PUCC protein	0.003

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

 Score =  123 bits (311), Expect = 1e-36
 Identities = 41/61 (67%), Positives = 49/61 (80%)

Query: 32 AEQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAK 91
             + L CPRC+S NTKFCYYNNYN +QPR+FCK+CRRYWT GG LR++PVGGG RKN +
Sbjct: 1  KPDKALKCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKR 60

Query: 92 R 92
           
Sbjct: 61 S 61

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

>gnl|CDD|217426 pfam03209, PUCC, PUCC protein

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 24/84 (28%), Positives = 31/84 (36%), Gaps = 17/84 (20%)

Query: 148 GYGVCGNGTGAGGFASLL--SPQGPGFL-ALGGFGLGLGSGFVGD-----------VGLA 193
           G+G      G   F +L+  +  G   L   G   +G G+G  G               A
Sbjct: 279 GWGCAV---GLPAFLALIFSALLGNVALFVAGTLLIGFGAGLFGHATLTAMMDLAPEERA 335

Query: 194 GLGRGAWGLAGVSDAGAAAANGGG 217
           G   GAWG A  + AG A   GG 
Sbjct: 336 GTALGAWGAAQATAAGLAILLGGV 359

This protein is required for high-level transcription of the PUC operon. Length = 402

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	262
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	94.07
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	94.02
COG3677	129	Transposase and inactivated derivatives [DNA repli	93.8
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	92.94
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	91.67
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	89.15
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	84.54
PHA02998	195	RNA polymerase subunit; Provisional	84.35
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	84.33
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	81.02

>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=1.1e-37  Score=232.19  Aligned_cols=62  Identities=76%  Similarity=1.534  Sum_probs=59.0

Q ss_pred             CCCCcCCCCCcCCCceeeeecccCCCCCcccccccccccccCcccccccCCCCcccCCCCCC
Q 024786           33 EQEQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRDIPVGGGTRKNAKRCR   94 (262)
Q Consensus        33 e~e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVGGG~RKnk~~s~   94 (262)
                      +++.++||||+|++|||||||||+++||||||++|+||||+||+|||||||||+||+|++++
T Consensus         2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~s   63 (63)
T PF02701_consen    2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSSS   63 (63)
T ss_pred             CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCCC
Confidence            56789999999999999999999999999999999999999999999999999999987653

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=94.07  E-value=0.027  Score=47.62  Aligned_cols=35  Identities=23%  Similarity=0.655  Sum_probs=27.5

Q ss_pred             CcCCCCCcCCCceeeeecccCC--CCCcccccccccccc
Q 024786           36 QLPCPRCESTNTKFCYYNNYNF--SQPRHFCKSCRRYWT   72 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~--~QPR~fCk~CrRyWT   72 (262)
                      ..+||||.|.+|+..  +.+-.  ++.-|+|++|+.=|.
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            479999999999964  55544  467799999997554

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=94.02  E-value=0.047  Score=37.51  Aligned_cols=29  Identities=38%  Similarity=0.839  Sum_probs=23.2

Q ss_pred             CCcCCCCCcCCCceeeeecccCCCCCccccccccc
Q 024786           35 EQLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRR   69 (262)
Q Consensus        35 e~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR   69 (262)
                      +...||+|.+.  +...+.+    +.+|.|++|++
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=93.80  E-value=0.043  Score=45.50  Aligned_cols=36  Identities=33%  Similarity=0.657  Sum_probs=28.5

Q ss_pred             CcCCCCCcCCCceeeeecccCCCCCccccccccccccc
Q 024786           36 QLPCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTH   73 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~   73 (262)
                      ...||+|.+.+  +-=+.-+.....||.|++|++-|+.
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  3335555555999999999999974

>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=92.94  E-value=0.066  Score=36.32  Aligned_cols=31  Identities=42%  Similarity=0.756  Sum_probs=21.8

Q ss_pred             CcCCCCCcCCCceeeeecccCCC-CCcccccccc
Q 024786           36 QLPCPRCESTNTKFCYYNNYNFS-QPRHFCKSCR   68 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr   68 (262)
                      .+.||+|.+++.-  |=|-.+.. ..||+|++|+
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  23444433 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=91.67  E-value=0.2  Score=34.14  Aligned_cols=37  Identities=24%  Similarity=0.753  Sum_probs=28.6

Q ss_pred             cCCCCCcCCCceeeeecccCCCCC---ccccccccccccc
Q 024786           37 LPCPRCESTNTKFCYYNNYNFSQP---RHFCKSCRRYWTH   73 (262)
Q Consensus        37 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRyWT~   73 (262)
                      .+||+|...+.-|-..+-.+...|   -|.|.+|...|..
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            379999988777766666666555   3999999999963

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

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

Probab=89.15  E-value=0.34  Score=32.73  Aligned_cols=35  Identities=23%  Similarity=0.692  Sum_probs=24.5

Q ss_pred             CCCCCcCCCceeeeecccCCCCCc---ccccccccccc
Q 024786           38 PCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWT   72 (262)
Q Consensus        38 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT   72 (262)
                      +||.|...+.-|--.+......|-   |.|.+|..-|+
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            799999988776555666555553   99999999985

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=84.54  E-value=0.44  Score=43.10  Aligned_cols=37  Identities=27%  Similarity=0.643  Sum_probs=18.4

Q ss_pred             CcCCCCCcCC-CceeeeecccCCCCC-cccccccccccc
Q 024786           36 QLPCPRCEST-NTKFCYYNNYNFSQP-RHFCKSCRRYWT   72 (262)
Q Consensus        36 ~~~CPRC~S~-nTKFcYyNNy~~~QP-R~fCk~CrRyWT   72 (262)
                      ...||.|..+ ..++-||..-....- -+.|..|+.|+-
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            3589999888 456777743333333 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=84.35  E-value=1  Score=40.83  Aligned_cols=41  Identities=29%  Similarity=0.699  Sum_probs=34.6

Q ss_pred             CCCCcCCCCCcCCCceeeeecccCCCCCc---cccccccccccc
Q 024786           33 EQEQLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTH   73 (262)
Q Consensus        33 e~e~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~   73 (262)
                      +....+||+|...++-|--.|-++-..|-   |.|..|..-|.-
T Consensus       140 kkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp  183 (195)
T PHA02998        140 EKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP  183 (195)
T ss_pred             cccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence            33568999999999999888888888885   899999999963

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=84.33  E-value=0.29  Score=32.87  Aligned_cols=37  Identities=27%  Similarity=0.605  Sum_probs=27.7

Q ss_pred             CCCCCcCCCceeeeecccCCCCCcccccccccccccCccccc
Q 024786           38 PCPRCESTNTKFCYYNNYNFSQPRHFCKSCRRYWTHGGTLRD   79 (262)
Q Consensus        38 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRn   79 (262)
                      +||+|...-...-+     ..-+-+.|.+|.-.|=..+.|..
T Consensus         1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~   37 (41)
T PF13453_consen    1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK   37 (41)
T ss_pred             CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence            69999987555444     23566889999999988777654

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=81.02  E-value=2.1  Score=33.07  Aligned_cols=39  Identities=18%  Similarity=0.603  Sum_probs=29.1

Q ss_pred             CcCCCCCcCCCceeeeecccCCCCCc---ccccccccccccC
Q 024786           36 QLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTHG   74 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~G   74 (262)
                      ..+||+|...+.-|-..|-.+-..|-   |.|..|.-.|+..
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            57999998777766555555544443   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.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	262
1tfi_A	50	Transcriptional elongation factor SII; transcripti	87.79
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	86.82

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

Probab=87.79  E-value=0.52  Score=32.59  Aligned_cols=39  Identities=18%  Similarity=0.632  Sum_probs=29.7

Q ss_pred             CCCcCCCCCcCCCceeeeecccCCCCCc---ccccccccccc
Q 024786           34 QEQLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWT   72 (262)
Q Consensus        34 ~e~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT   72 (262)
                      ....+||+|...+..|--.+..+...|-   |.|..|..-|.
T Consensus         7 t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~   48 (50)
T 1tfi_A            7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             eCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence            3456899999888777666666665564   89999998885

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

Probab=86.82  E-value=0.43  Score=32.87  Aligned_cols=38  Identities=18%  Similarity=0.581  Sum_probs=26.1

Q ss_pred             CcCCCCCcCCCceeeeecccCCCCC---ccccccccccccc
Q 024786           36 QLPCPRCESTNTKFCYYNNYNFSQP---RHFCKSCRRYWTH   73 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRyWT~   73 (262)
                      .++||+|...+..|--.+-.....|   .|.|..|.--|..
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            5789999984444443343344445   3999999999975

---

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	262
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	91.69
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	91.52
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	85.01

>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=91.69  E-value=0.065  Score=36.11  Aligned_cols=38  Identities=18%  Similarity=0.649  Sum_probs=32.2

Q ss_pred             CCcCCCCCcCCCceeeeecccCCCCCc---ccccccccccc
Q 024786           35 EQLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWT   72 (262)
Q Consensus        35 e~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT   72 (262)
                      ..++||+|.+.+..|--.|..+...|-   +.|..|..-|-
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            457999999999888777888777776   99999999883

>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=91.52  E-value=0.1  Score=37.25  Aligned_cols=41  Identities=22%  Similarity=0.488  Sum_probs=32.1

Q ss_pred             CcCCCCCcCCCceeeeecccCCCCCc---ccccccccccccCcc
Q 024786           36 QLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTHGGT   76 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~GGt   76 (262)
                      ...||+|...+.-|-+.+-.+..-|-   |.|..|.-.|+...+
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            46999999888877777666555554   999999999998543

>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=85.01  E-value=0.27  Score=33.51  Aligned_cols=38  Identities=18%  Similarity=0.607  Sum_probs=29.3

Q ss_pred             CcCCCCCcCCCceeeeecccCCCCCc---cccccccccccc
Q 024786           36 QLPCPRCESTNTKFCYYNNYNFSQPR---HFCKSCRRYWTH   73 (262)
Q Consensus        36 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~   73 (262)
                      .++||+|...+.-|--.|-....-|-   |.|..|..-|..
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            36899999888877666665555554   899999999863