Citrus Sinensis ID: 040161

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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-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360------
Protein Sequence
MIQELLGAAGFISGDRKISITGSIFEGTTSPLPPCTTTTTATVTTTTATAAPPPPPPPLPTTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVTAASFGKSSSSSSAANKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP
Secondary Structure (PSIPRED)
cHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccEEcccccccccccEEcccccccHHHHcccccccccccccccccccHHcHHHcccccccccccccEEEEcEccccHHHHHHHHHcccccccccccccccEEEEcccccccHHHcccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MIQELLGaagfisgdrkisitgsifegttsplppctttttatvttttataappppppplpttttsntdsnignntnntssnsgnnqnlrcprcdssntkfcyynnynltqprhfcKTCRrywtkggalrnvpigggcrknkssstvtaasfgkssssssaANKMKTVAYEIgrggfvhhpheyysstpimwnnsphnSQLLALLRtsqnpninptgpststssvrvkeeqgvigthhvikgepvgdtaavlnsgtmvfnplsqqlqvpsqlglwknnqhqiqapqqngflvgheVQNSGVQELYQRFKSstnnyyadhlaspvvlsnaasstttilesapvaggelgywnpvfswsdlsttngsyp
Flexible Loop (DISEMBL)
MIQELLGAagfisgdrkISITGSifegttsplppcTTTTTATVTTTtataapppppppLPTTTTSNTDSNIGNNTnntssnsgnnqnlRCPRCDSSNTKFCYYNnynltqprhfCKTCRRYWTKGGalrnvpigggcrknkssSTVTAasfgkssssssaanKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNInptgpststssvrVKEEQGVIgthhvikgepvGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNpvfswsdlsttngsyp
Low Complexity Region (SEG)
MIQELLGAAGFISGDRKISITGSIFEGttsplppctttttatvttttataappppppplpttttsntdsnignntnntssnsgnnQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVTaasfgkssssssaaNKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNplsqqlqvpsqlglWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP
Disordered region (IsUnstruct)
*****LGAAGFISGDRKISITGSIFEGT*******************************************************************SNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGC****************************TVAYEIGRGGFVHHPHEYYSSTPIMWNN**************************************VIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSD*********
Disordered Region (DISOPRED)
*******************************************************************************************RCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRN*************************************************************************************************************************************************************************************************************************YWNPVFSWSDLSTT*****
Disordered Region (DISEMBL)
MIQELLGAAGFISGDRKISITGSIFEGTTSPLPPCTTTTTATVT************PPLPTTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGC************************NKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINP*************EEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP
Disordered Region (DISPRO)
*IQ*LLGAAGFIS*************************************************************************NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIG****************************************GFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTN****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIQELLGAAGFISGDRKISITGSIFEGTTSPLPPCTTTTTATVTTTTATAAPPPPPPPLPTTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVTAASFGKSSSSSSAANKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP
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	366	2.2.26 [Sep-21-2011]
Q84TE9	257	Dof zinc finger protein D	yes	no	0.248	0.354	0.595	5e-28
Q9LSL6	316	Dof zinc finger protein D	no	no	0.259	0.300	0.602	9e-28
Q8LDR0	307	Dof zinc finger protein D	no	no	0.199	0.237	0.687	2e-27
Q8L9V6	331	Dof zinc finger protein D	no	no	0.144	0.160	0.905	4e-27
Q9ZV33	340	Dof zinc finger protein D	no	no	0.142	0.152	0.865	2e-26
O80928	330	Dof zinc finger protein D	no	no	0.147	0.163	0.833	3e-26
O24463	328	Dof zinc finger protein P	N/A	no	0.177	0.198	0.723	5e-26
Q9M1E6	245	Dof zinc finger protein D	no	no	0.174	0.261	0.75	7e-26
Q9LZ56	399	Dof zinc finger protein D	no	no	0.147	0.135	0.833	1e-25
Q9M2U1	323	Dof zinc finger protein D	no	no	0.172	0.195	0.730	2e-25

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

 Score =  125 bits (314), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 56/94 (59%), Positives = 71/94 (75%), Gaps = 3/94 (3%)

Query: 88  LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVT 147
           LRCPRCDS+NTKFCYYNNY+LTQPR+FCK+CRRYWTKGG LRN+P+GGGCRKNK S++  
Sbjct: 55  LRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPVGGGCRKNKRSTSSA 114

Query: 148 AASFGKSSSSSSAANKMKTVAYEIGRGGFVHHPH 181
           A S   +   +S   K+ + A   G  G+ ++ H
Sbjct: 115 ARSLRTTPEPASHDGKVFSAA---GFNGYSNNEH 145

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

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

 Score =  124 bits (312), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 59/98 (60%), Positives = 70/98 (71%), Gaps = 3/98 (3%)

Query: 46  TTATAAPPPPPPPLPTTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNN 105
           ++ T  P P P P P    S T          +SS + + QNL+CPRC+S NTKFCYYNN
Sbjct: 2   SSHTNLPSPKPVPKPDHRISGTSQT---KKPPSSSVAQDQQNLKCPRCNSPNTKFCYYNN 58

Query: 106 YNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSS 143
           Y+L+QPRHFCK+CRRYWT+GGALRNVPIGGGCRK K S
Sbjct: 59  YSLSQPRHFCKSCRRYWTRGGALRNVPIGGGCRKTKKS 96

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 =  123 bits (308), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 55/80 (68%), Positives = 64/80 (80%), Gaps = 7/80 (8%)

Query: 84  NNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSS 143
           ++Q+L+CPRC+S NTKFCYYNNYNL+QPRHFCK CRRYWTKGG LRNVP+GGGCRK K S
Sbjct: 47  HHQSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKAKRS 106

Query: 144 STVTAASFGKSSSSSSAANK 163
            T       K   SSS+A+K
Sbjct: 107 KT-------KQVPSSSSADK 119

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 =  122 bits (306), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 48/53 (90%), Positives = 52/53 (98%)

Query: 88  LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKN 140
           L+CPRCDSSNTKFCYYNNYNLTQPRHFCK CRRYWT+GGALRNVP+GGGCR+N
Sbjct: 77  LKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRN 129

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

 Score =  120 bits (301), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 45/52 (86%), Positives = 51/52 (98%)

Query: 88  LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRK 139
           L+CPRCDS+NTKFCY+NNYNLTQPRHFCK CRRYWT+GGALRNVP+GGGCR+
Sbjct: 94  LKCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPVGGGCRR 145

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 =  119 bits (298), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 45/54 (83%), Positives = 54/54 (100%)

Query: 88  LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK 141
           L+CPRC+S+NTKFCY+NNY+LTQPRHFCKTCRRYWT+GGALRNVP+GGGCR+N+
Sbjct: 89  LKCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNR 142

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 =  119 bits (297), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 47/65 (72%), Positives = 55/65 (84%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           + L+CPRCDS+NTKFCYYNNY+++QPR+FCK CRRYWT GG LRNVPIGGGCRKNK +S 
Sbjct: 58  EALKCPRCDSNNTKFCYYNNYSMSQPRYFCKACRRYWTHGGTLRNVPIGGGCRKNKHASR 117

Query: 146 VTAAS 150
               S
Sbjct: 118 FVLGS 122

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|Q9M1E6|DOF32_ARATH Dof zinc finger protein DOF3.2 OS=Arabidopsis thaliana GN=DOF3.2 PE=2 SV=1

 Score =  118 bits (296), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 48/64 (75%), Positives = 58/64 (90%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           Q+LRCPRCDS+NTKFCYYNNY+L+QPR+FCK+CRRYWTKGG LRN+PIGG  RK+K SS+
Sbjct: 38  QSLRCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGILRNIPIGGAYRKHKRSSS 97

Query: 146 VTAA 149
            T +
Sbjct: 98  ATKS 101

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LZ56|DOF51_ARATH Dof zinc finger protein DOF5.1 OS=Arabidopsis thaliana GN=DOF5.1 PE=2 SV=1

 Score =  117 bits (294), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 45/54 (83%), Positives = 53/54 (98%)

Query: 88  LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK 141
           L+CPRCDS+NTKFCY+NNY+LTQPRHFCK CRRYWT+GGALR+VP+GGGCR+NK
Sbjct: 95  LKCPRCDSTNTKFCYFNNYSLTQPRHFCKACRRYWTRGGALRSVPVGGGCRRNK 148

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M2U1|DOF36_ARATH Dof zinc finger protein DOF3.6 OS=Arabidopsis thaliana GN=DOF3.6 PE=1 SV=2

 Score =  117 bits (292), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 57/63 (90%)

Query: 88  LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVT 147
           L CPRCDS+NTKFCY+NNY+LTQPRHFCKTCRRYWT+GG+LRNVP+GGG R+NK S + +
Sbjct: 76  LNCPRCDSTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGSLRNVPVGGGFRRNKRSKSRS 135

Query: 148 AAS 150
            ++
Sbjct: 136 KST 138

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)

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	366
224096832	323	f-box family protein [Populus trichocarp	0.691	0.783	0.647	7e-85
255562669	335	zinc finger protein, putative [Ricinus c	0.710	0.776	0.651	8e-81
359496061	332	PREDICTED: uncharacterized protein LOC10	0.710	0.783	0.589	1e-74
147795426	309	hypothetical protein VITISV_028751 [Viti	0.666	0.789	0.571	5e-73
297735843	425	unnamed protein product [Vitis vinifera]	0.710	0.611	0.551	5e-71
302398781	346	DOF domain class transcription factor [M	0.721	0.763	0.528	1e-64
356563674	352	PREDICTED: uncharacterized protein LOC77	0.713	0.741	0.516	1e-60
449448350	334	PREDICTED: dof zinc finger protein DOF3.	0.855	0.937	0.478	3e-60
224081545	269	f-box family protein [Populus trichocarp	0.715	0.973	0.447	3e-60
356496846	336	PREDICTED: uncharacterized protein LOC77	0.901	0.982	0.443	5e-55

>gi|224096832|ref|XP_002310753.1| f-box family protein [Populus trichocarpa] gi|118482074|gb|ABK92968.1| unknown [Populus trichocarpa] gi|222853656|gb|EEE91203.1| f-box family protein [Populus trichocarpa]

 Score =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 187/289 (64%), Positives = 215/289 (74%), Gaps = 36/289 (12%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK++S 
Sbjct: 63  ENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKNTS- 121

Query: 146 VTAASFGKSSSSSSAANKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLR 205
             +AS GKS +     NKMKT+A +IGR GF +      SS+PIMW  SP NS +LALLR
Sbjct: 122 -VSASVGKSGT-----NKMKTMASDIGRSGFGNGFEHELSSSPIMW-ASPQNSHILALLR 174

Query: 206 TSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQL 265
            +QNPN     PST ++S+ VKEE G+IG   +   EP   TAA LN+ T+  +P+S   
Sbjct: 175 ATQNPN-----PSTLSNSIFVKEEGGLIGNQFI--SEPGVGTAA-LNARTLGLDPIS--- 223

Query: 266 QVPSQLGL----WKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLAS 321
           QVPS LGL    WK+NQH     QQNGF VG E QNSG+QELYQR +SST NYY D+  S
Sbjct: 224 QVPS-LGLCSPFWKSNQH-----QQNGFTVG-EAQNSGIQELYQRLRSST-NYYTDN-PS 274

Query: 322 PVVLSNAA----SSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP 366
            +VLSN A    +ST+TILESAPVAGGELGYWNP FSWSDL TTNG+YP
Sbjct: 275 AIVLSNVATSSSTSTSTILESAPVAGGELGYWNPAFSWSDLPTTNGAYP 323

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562669|ref|XP_002522340.1| zinc finger protein, putative [Ricinus communis] gi|223538418|gb|EEF40024.1| zinc finger protein, putative [Ricinus communis]

 Score =  306 bits (785), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 189/290 (65%), Positives = 215/290 (74%), Gaps = 30/290 (10%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK  +T
Sbjct: 67  ENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK--NT 124

Query: 146 VTAASFGKSSSSSSAANKMKTVAYEIGRGGFVH-HPHEYYSSTPIMWNNSPHNSQLLALL 204
           V +AS  KSS+     NKMKT+  EIGR  F +   HE  SS+PIMW  SPHNS LL LL
Sbjct: 125 VVSASVAKSSN-----NKMKTMVSEIGRSSFGNVFDHELPSSSPIMW-ASPHNSHLLTLL 178

Query: 205 RTSQNPNINPTGPSTSTSSVRVKEEQG-VIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQ 263
           R + NPN N T   T ++S+ VKEE G +IGT   +  E  G T A LN+ T+  + LS 
Sbjct: 179 RANHNPNPNST---TLSNSLGVKEETGCMIGTQ--MMAETTGATGA-LNARTLGMDHLS- 231

Query: 264 QLQVPSQLGL----WKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHL 319
             QVPS LGL    WKN+Q+Q Q  QQNGF+VG E QNSG+QELYQR +SSTN YY D+ 
Sbjct: 232 --QVPS-LGLCSPFWKNSQNQAQHHQQNGFIVG-EAQNSGIQELYQRLRSSTNTYYTDN- 286

Query: 320 ASPVVLSNAASSTTT---ILESAPVAGGELGYWNPVFSWSDLSTTNGSYP 366
            S VVLSN  SS+T+   ILES+PVAGGELGYWNP FSWSDL TTNG+YP
Sbjct: 287 -SSVVLSNVGSSSTSSSNILESSPVAGGELGYWNPTFSWSDLPTTNGAYP 335

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496061|ref|XP_003635142.1| PREDICTED: uncharacterized protein LOC100244391 [Vitis vinifera]

 Score =  286 bits (732), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 172/292 (58%), Positives = 202/292 (69%), Gaps = 32/292 (10%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK++S 
Sbjct: 62  ENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKNTSV 121

Query: 146 VTAASFGKSSSSSSAANKMKTVAYEIGR----GGFVHHPHEYYSSTPIMWNNSPHNSQLL 201
            TA   GKSS     A K K+   EIG+    GGF H       S PI+W  SP NS LL
Sbjct: 122 STAV--GKSS-----AGKAKSAVSEIGKSGLGGGFDHE----IPSNPILW-ASPQNSHLL 169

Query: 202 ALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPL 261
           ALLR +QNPN N   PS  ++SV VK++  +IG+H  +  E    T AV  +  M  + L
Sbjct: 170 ALLRATQNPNPN---PSPISNSVTVKDDGVMIGSH--MTSESGVGTGAVNIARNMGLDHL 224

Query: 262 SQQLQVPSQLGLWK-------NNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNY 314
           +Q   +      W+        +Q      QQNGF++G EVQN+G+QELYQR +SST NY
Sbjct: 225 NQLPSIGLCSSYWRNNQHQTQQHQQNSHHQQQNGFILG-EVQNTGIQELYQRLRSST-NY 282

Query: 315 YADHLASPVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP 366
           Y DH  SPVVLSNA SS+++ILESAP+AGGELGYWNP FSWSDL TTNG+YP
Sbjct: 283 YTDH--SPVVLSNAVSSSSSILESAPIAGGELGYWNPTFSWSDLPTTNGAYP 332

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147795426|emb|CAN72540.1| hypothetical protein VITISV_028751 [Vitis vinifera]

 Score =  280 bits (717), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 163/285 (57%), Positives = 194/285 (68%), Gaps = 41/285 (14%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK++S 
Sbjct: 62  ENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKNTSV 121

Query: 146 VTAASFGKSSSSSSAANKMKTVAYEIGR----GGFVHHPHEYYSSTPIMWNNSPHNSQLL 201
            TA   GKSS     A K K+   EIG+    GGF H       S PI+W  SP NS LL
Sbjct: 122 STAV--GKSS-----AGKAKSAVSEIGKSGLGGGFDHE----IPSNPILW-ASPQNSHLL 169

Query: 202 ALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPL 261
           ALLR +QNPN N   PS  ++SV VK++  +IG+H  +  E    TA    +  +  N  
Sbjct: 170 ALLRATQNPNPN---PSPISNSVTVKDDGVMIGSH--MTSESGVGTALTGETINIKLNST 224

Query: 262 SQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNYYADHLAS 321
           ++   + S++ L               +LV  + QN+G+QELYQR +SST NYY DH  S
Sbjct: 225 NKTATINSKMAL---------------YLV--KFQNTGIQELYQRLRSST-NYYTDH--S 264

Query: 322 PVVLSNAASSTTTILESAPVAGGELGYWNPVFSWSDLSTTNGSYP 366
           PVVLSNA SS+++ILESAP+AGGELGYWNP FSWSDL TTNG+YP
Sbjct: 265 PVVLSNAVSSSSSILESAPIAGGELGYWNPTFSWSDLPTTNGAYP 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735843|emb|CBI18563.3| unnamed protein product [Vitis vinifera]

 Score =  274 bits (700), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 172/312 (55%), Positives = 202/312 (64%), Gaps = 52/312 (16%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK++S 
Sbjct: 135 ENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKNTSV 194

Query: 146 VTAASFGKSSSSSSAANKMKTVAYEIGR----GGFVHHPHEYYSSTPIMWNNSPHNSQLL 201
            TA   GKSS     A K K+   EIG+    GGF H       S PI+W  SP NS LL
Sbjct: 195 STAV--GKSS-----AGKAKSAVSEIGKSGLGGGFDHE----IPSNPILW-ASPQNSHLL 242

Query: 202 ALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVFNPL 261
           ALLR +QNPN N   PS  ++SV VK++  +IG+H  +  E    T AV  +  M  + L
Sbjct: 243 ALLRATQNPNPN---PSPISNSVTVKDDGVMIGSH--MTSESGVGTGAVNIARNMGLDHL 297

Query: 262 SQQLQVPSQLGLWK-------NNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSSTNNY 314
           +Q   +      W+        +Q      QQNGF++G EVQN+G+QELYQR +SST NY
Sbjct: 298 NQLPSIGLCSSYWRNNQHQTQQHQQNSHHQQQNGFILG-EVQNTGIQELYQRLRSST-NY 355

Query: 315 YADHLASPV--------------------VLSNAASSTTTILESAPVAGGELGYWNPVFS 354
           Y DH  SPV                    VLSNA SS+++ILESAP+AGGELGYWNP FS
Sbjct: 356 YTDH--SPVVLSNAVSSSSSILESAPIAGVLSNAVSSSSSILESAPIAGGELGYWNPTFS 413

Query: 355 WSDLSTTNGSYP 366
           WSDL TTNG+YP
Sbjct: 414 WSDLPTTNGAYP 425

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302398781|gb|ADL36685.1| DOF domain class transcription factor [Malus x domestica]

 Score =  253 bits (646), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 160/303 (52%), Positives = 200/303 (66%), Gaps = 39/303 (12%)

Query: 84  NNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSS 143
           N +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGG RKNKS 
Sbjct: 61  NTENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGYRKNKSV 120

Query: 144 STVTAASFGKSSSSSSAANKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLAL 203
           +  TA      S   +AA K+KTV  EIGR GF     +   ++PI+W  SP NS LLAL
Sbjct: 121 TGSTA------SIDKTAAGKLKTVVSEIGRSGFGAGFDQEVQASPILW-GSPQNSHLLAL 173

Query: 204 LRTS--QNPNINPTGPSTSTSSVRVKEEQG--VIGTHHVIKGEPVGDTAAVLNSGTMVFN 259
           L+ S  QNPN     P+   +SV VKEE G  +IG+H +       +  A+  + T+  +
Sbjct: 174 LKASHHQNPN-----PNQLCNSVNVKEEGGMNMIGSHMMTT-----EAIAMSTARTLGLD 223

Query: 260 PLSQQLQVPSQLGLWKNNQHQIQAP----QQNGFLVGHEVQNS--GVQELYQRFKSSTN- 312
           P+ Q   +      W+NN +Q Q P    QQNGF+VGHEVQ+S  G+QEL+QR   ST+ 
Sbjct: 224 PVCQAPSLGLCSSFWRNN-NQDQPPPSHHQQNGFIVGHEVQSSNIGIQELFQRLTPSTSQ 282

Query: 313 --NYYADHLASPVV----LSNAASSTTTILESAP-VAGGELGY-WNPVF-SWS-DLSTTN 362
             +YY+D L + V      S ++ ST++IL+S+P V GGE+GY WNP F +WS DL TTN
Sbjct: 283 SCSYYSDQLNNVVASSSSSSLSSYSTSSILDSSPVVGGGEMGYSWNPAFTAWSFDLPTTN 342

Query: 363 GSY 365
           G+Y
Sbjct: 343 GAY 345

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356563674|ref|XP_003550086.1| PREDICTED: uncharacterized protein LOC778108 [Glycine max]

 Score =  240 bits (612), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 155/300 (51%), Positives = 195/300 (65%), Gaps = 39/300 (13%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           +NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKS   
Sbjct: 73  ENLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSIGV 132

Query: 146 VTAASFGKSSSSSSAANKMKTVAYEIGR----GGFVHHPHEY-YSSTPIMWNNSPHNSQL 200
            ++ + GK++S+     KMKT+A E G+    GG     HE       I+W  SP N+ L
Sbjct: 133 ASSVA-GKTAST-----KMKTIASEFGKSPGFGGGFEVEHELPPPPGQILW-GSPQNTHL 185

Query: 201 LALLRT--SQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIKGEPVGDTAAVLNSGTMVF 258
           LALLR   +QNPN NP       S + +KEE  ++G H V   +P+  +  +L+  T+ +
Sbjct: 186 LALLRATQTQNPNPNP-------SPMSLKEEGTLLG-HMVSTDQPL-VSNTLLSYRTLGY 236

Query: 259 NPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGVQELYQRFKSST---NNYY 315
           + ++   QVPS LGL+    +Q Q  Q  GFLVG    NSG+QELYQ+ +SS+   NNY 
Sbjct: 237 DAVA---QVPSSLGLF-GRNNQDQQQQNGGFLVGEHHNNSGIQELYQKLRSSSTVNNNYC 292

Query: 316 ADHLASPVVLSNAA-----SSTTTILESAPVAGGELGYWN-PVFS-WSDLSTTN--GSYP 366
           +D+ +S + + N A     S +  ILE+  VAGGE GYWN P FS WSDL TTN  G+YP
Sbjct: 293 SDNNSSQMFMGNMASNYSSSVSNNILETTSVAGGEFGYWNGPTFSNWSDLPTTNGAGAYP 352

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448350|ref|XP_004141929.1| PREDICTED: dof zinc finger protein DOF3.7-like [Cucumis sativus] gi|449485454|ref|XP_004157173.1| PREDICTED: dof zinc finger protein DOF3.7-like [Cucumis sativus]

 Score =  238 bits (608), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 185/387 (47%), Positives = 230/387 (59%), Gaps = 74/387 (19%)

Query: 1   MIQELLGAAGFIS--GDRKISI--TGSIFEGTTSPLPPCTTTTTATVTTTTATAAPPPPP 56
           MIQEL G +G ++  GD KISI  T SI + + S     + T  +  T TT         
Sbjct: 1   MIQELFGVSGLLAAAGDTKISINNTCSILDSSPSTSLSASATAASNATVTTTATP----- 55

Query: 57  PPLPTTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCK 116
                                T+S++   QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCK
Sbjct: 56  ---------------------TTSSNSEGQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCK 94

Query: 117 TCRRYWTKGGALRNVPIGGGCRKNKSSSTVTAASFGKSSSSSSAANKMKTVAYEI-GRGG 175
           TCRRYWTKGGALRNVPIGGGCRKNKS++   AA+ GKS+S      KMKT++ EI GR G
Sbjct: 95  TCRRYWTKGGALRNVPIGGGCRKNKSAAATVAAAVGKSTSG-----KMKTLSSEILGRVG 149

Query: 176 FVHH---PHEYYSS-TPIMWNNSPHNSQLLALLRTS-QNPNINPTGPSTSTSSVRVKEEQ 230
           F +     HE  SS T I+W  SP NS LLA+LR++ QNPN     PS  T+S       
Sbjct: 150 FGNGSALDHEIISSPTQILW-GSPQNSHLLAILRSATQNPN-----PSNLTAS------- 196

Query: 231 GVIGTHHVIKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGL----WKNNQHQIQAPQQ 286
                 HVI  +P   T    ++ TM F+       V S LGL    W+NNQ+Q+   QQ
Sbjct: 197 ------HVINNDPPPSTTP-FHARTMGFDDPPAGPHV-SSLGLCSSYWRNNQNQVHH-QQ 247

Query: 287 NGFLVGHEVQ----NSGVQELYQRFKSSTNNYYAD-HLASPVVLSNAASSTTTILESAPV 341
           NG+  G   Q     SG+QELYQ+ KSS+NNY++D H  S  V + A ++T  ILE+APV
Sbjct: 248 NGYPHGGGDQVHSGASGIQELYQKLKSSSNNYFSDSHQGSVGVTNVATTATAAILEAAPV 307

Query: 342 AGGEL-GYWNPVFSWSDL-STTNGSYP 366
            GGE+ G+WNP FSWSD+ ++ NG+YP
Sbjct: 308 GGGEMTGFWNPAFSWSDVHASANGAYP 334

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081545|ref|XP_002306453.1| f-box family protein [Populus trichocarpa] gi|222855902|gb|EEE93449.1| f-box family protein [Populus trichocarpa]

 Score =  238 bits (607), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 167/373 (44%), Positives = 199/373 (53%), Gaps = 111/373 (29%)

Query: 1   MIQELLGAAGFISGDRKISITGSIFEGTTSPLPPCTTTTTATVTTTTATAAPPPPPPPLP 60
           MIQELLG AG ISG+RKI I  +I +       P ++TTT T  T +  +A         
Sbjct: 1   MIQELLGGAGLISGERKIPINATILDQGAPSPSPSSSTTTTTSATNSTPSA--------- 51

Query: 61  TTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 120
                                    + LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR
Sbjct: 52  ------------------------QEKLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR 87

Query: 121 YWTKGGALRNVPIGGGCRKNKSSSTVTAASFGKSSSSSSAANKMKTVAYEIGRGGFVHHP 180
           YWTKGGALRNVPIGGGCRKNK++S   +AS GKS +S     K+KT+A EIGR GF +  
Sbjct: 88  YWTKGGALRNVPIGGGCRKNKNTS--VSASVGKSGTS-----KIKTIASEIGRSGFGNGF 140

Query: 181 HEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHVIK 240
               SS+PIM   SP NS + ALLR +QNPN     PST  +S+ VK+E  +IG H + +
Sbjct: 141 DYELSSSPIM-RASPQNSHIFALLRATQNPN-----PSTPCNSISVKQEGFLIGKHMITQ 194

Query: 241 GEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNSGV 300
                      NSG      L Q+L+                                  
Sbjct: 195 -----------NSG---IQELYQRLR---------------------------------- 206

Query: 301 QELYQRFKSSTNNYYADHLASPVVLSNA-------ASSTTTILESAPVAGGELGYWNPVF 353
                   SSTN YY D+  S +VLSN         S+++TILESAPVAGGE  YWN  F
Sbjct: 207 --------SSTN-YYTDN-PSAIVLSNVTTSSSTSTSTSSTILESAPVAGGEFSYWNQAF 256

Query: 354 SWSDLSTTNGSYP 366
           SWS L TTNG+YP
Sbjct: 257 SWSGLPTTNGAYP 269

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496846|ref|XP_003517276.1| PREDICTED: uncharacterized protein LOC778100 [Glycine max]

 Score =  221 bits (562), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 165/372 (44%), Positives = 215/372 (57%), Gaps = 42/372 (11%)

Query: 1   MIQELLG--AAGFISGDRKISITGSIFEGTTSPLPPCTTTTTATVTTTTATAAPPPPPPP 58
           MIQELLG  +A  I+G+RKISIT                            A    PP  
Sbjct: 1   MIQELLGGASASLIAGERKISIT------------------------NGGGALLLTPPTS 36

Query: 59  LPTTTTSNTDSNIGNNTNNTSSNSGNNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTC 118
              + + +  ++I  +T   +S++  NQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTC
Sbjct: 37  SSPSLSPSCTTSITTSTATATSSNSENQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTC 96

Query: 119 RRYWTKGGALRNVPIGGGCRKNKSSSTVTAASFGKSSSSSSAANKMKTVAYEIGRGGFVH 178
           RRYWTKGGALRNVPIGGGCRK+KSS          +S +   A KMK VA E+GR     
Sbjct: 97  RRYWTKGGALRNVPIGGGCRKSKSSGM-------SNSVAKQTATKMKAVASELGRSSSQG 149

Query: 179 HPHEYYSSTPIMWNNSPHNSQLLALLRTSQNPNINPTGPSTSTSSVRVKEEQGVIGTHHV 238
              +    TP +   SP NSQL+ALLR +QN N NP     S  S+ VK E  ++G+HH+
Sbjct: 150 LLDQELPQTPAILWGSPQNSQLMALLRANQNHNPNPN---PSPMSIVVKGEGNLMGSHHM 206

Query: 239 IKGEPVGDTAAVLNSGTMVFNPLSQQLQVPSQLGLWKNNQHQIQAPQQNGFLVGHEVQNS 298
           +  EP+     +    ++ F+ + + L      G +  N       Q NGF +G E Q+S
Sbjct: 207 V-AEPLLANGLLNPRTSLGFDGVGEVLPSLGLCGSFWRNNQDQTQQQNNGFALG-EHQSS 264

Query: 299 GVQELYQRFKSSTNNY-YADHLASPVV---LSNAASSTTTILESAPVAGGELGYWNPVFS 354
           GVQELY + +SS+++  Y     SPV    +++++SS + ILES+ V+G E G WNP  S
Sbjct: 265 GVQELYHKLRSSSSSINYCGSDNSPVFLSNMASSSSSLSNILESSSVSGSEFGCWNPTLS 324

Query: 355 WSDLSTTNGSYP 366
           WSDL TTNG+YP
Sbjct: 325 WSDLPTTNGAYP 336

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	366
TAIR|locus:2155755	316	AT5G65590 [Arabidopsis thalian	0.158	0.183	0.844	8.6e-30
TAIR|locus:2053175	340	AT2G28810 [Arabidopsis thalian	0.158	0.170	0.810	2.3e-29
TAIR|locus:2159275	307	OBP4 "OBF binding protein 4" [	0.163	0.195	0.816	3.7e-29
TAIR|locus:2094746	204	DOF2 "DOF zinc finger protein	0.218	0.392	0.612	9.6e-29
TAIR|locus:2085697	245	DOF6 "DOF transcription factor	0.169	0.253	0.774	1.6e-28
TAIR|locus:2181773	399	AT5G02460 [Arabidopsis thalian	0.147	0.135	0.833	4.1e-28
TAIR|locus:2144030	257	TMO6 "TARGET OF MONOPTEROS 6"	0.248	0.354	0.563	2.8e-27
TAIR|locus:2079492	324	DAG1 "dof affecting germinatio	0.163	0.185	0.75	5.8e-27
TAIR|locus:2026595	339	OBP2 [Arabidopsis thaliana (ta	0.357	0.386	0.445	7.3e-27
TAIR|locus:2074850	253	OBP1 "OBF binding protein 1" [	0.163	0.237	0.754	4e-26

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

 Score = 303 (111.7 bits), Expect = 8.6e-30, Sum P(2) = 8.6e-30
 Identities = 49/58 (84%), Positives = 55/58 (94%)

Query:    86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSS 143
             QNL+CPRC+S NTKFCYYNNY+L+QPRHFCK+CRRYWT+GGALRNVPIGGGCRK K S
Sbjct:    39 QNLKCPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGALRNVPIGGGCRKTKKS 96

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

 Score = 302 (111.4 bits), Expect = 2.3e-29, Sum P(2) = 2.3e-29
 Identities = 47/58 (81%), Positives = 54/58 (93%)

Query:    88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
             L+CPRCDS+NTKFCY+NNYNLTQPRHFCK CRRYWT+GGALRNVP+GGGCR+NK   +
Sbjct:    94 LKCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPVGGGCRRNKKGKS 151

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 = 301 (111.0 bits), Expect = 3.7e-29, Sum P(2) = 3.7e-29
 Identities = 49/60 (81%), Positives = 54/60 (90%)

Query:    86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
             Q+L+CPRC+S NTKFCYYNNYNL+QPRHFCK CRRYWTKGG LRNVP+GGGCRK K S T
Sbjct:    49 QSLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKAKRSKT 108

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 = 298 (110.0 bits), Expect = 9.6e-29, Sum P(2) = 9.6e-29
 Identities = 49/80 (61%), Positives = 57/80 (71%)

Query:    86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
             + L+CPRCDS NTKFCYYNNYNL+QPRHFCK+CRRYWTKGGALRNVP+GGG RKN +  +
Sbjct:    27 EQLKCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALRNVPVGGGSRKNATKRS 86

Query:   146 VTXXXXXXXXXXXXXXNKMK 165
              +               K K
Sbjct:    87 TSSSSSASSPSNSSQNKKTK 106

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

 Score = 292 (107.8 bits), Expect = 1.6e-28, Sum P(2) = 1.6e-28
 Identities = 48/62 (77%), Positives = 57/62 (91%)

Query:    86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
             Q+LRCPRCDS+NTKFCYYNNY+L+QPR+FCK+CRRYWTKGG LRN+PIGG  RK+K SS+
Sbjct:    38 QSLRCPRCDSTNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGILRNIPIGGAYRKHKRSSS 97

Query:   146 VT 147
              T
Sbjct:    98 AT 99

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:2181773 AT5G02460 [Arabidopsis thaliana (taxid:3702)]

 Score = 291 (107.5 bits), Expect = 4.1e-28, Sum P(2) = 4.1e-28
 Identities = 45/54 (83%), Positives = 53/54 (98%)

Query:    88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNK 141
             L+CPRCDS+NTKFCY+NNY+LTQPRHFCK CRRYWT+GGALR+VP+GGGCR+NK
Sbjct:    95 LKCPRCDSTNTKFCYFNNYSLTQPRHFCKACRRYWTRGGALRSVPVGGGCRRNK 148

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 = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 53/94 (56%), Positives = 66/94 (70%)

Query:    88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVT 147
             LRCPRCDS+NTKFCYYNNY+LTQPR+FCK+CRRYWTKGG LRN+P+GGGCRKNK S++  
Sbjct:    55 LRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPVGGGCRKNKRSTSSA 114

Query:   148 XXXXXXXXXXXXXXNKMKTVAYEIGRGGFVHHPH 181
                            K+ + A   G  G+ ++ H
Sbjct:   115 ARSLRTTPEPASHDGKVFSAA---GFNGYSNNEH 145

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:2079492 DAG1 "dof affecting germination 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 5.8e-27, Sum P(2) = 5.8e-27
 Identities = 45/60 (75%), Positives = 54/60 (90%)

Query:    86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
             + + CPRC+S+NTKFCYYNNY+LTQPR+FCK CRRYWT+GG+LRNVP+GG  RKNK SST
Sbjct:    72 EKVNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGSSRKNKRSST 131

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009845 "seed germination" evidence=IMP

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

GO:0009639 "response to red or far red light" evidence=IMP

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

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 61/137 (44%), Positives = 77/137 (56%)

Query:    88 LRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSSTVT 147
             L+CPRCDSSNTKFCYYNNYNLTQPRHFCK CRRYWT+GGALRNVP+GGGCR+N       
Sbjct:    85 LKCPRCDSSNTKFCYYNNYNLTQPRHFCKGCRRYWTQGGALRNVPVGGGCRRNNKKGK-- 142

Query:   148 XXXXXXXXXXXXXXNKMKTVAYEIGRGGFVHHPHEYYSSTPIMWNNSPHNSQLLALLRTS 207
                            +  +V  +    G +   H++  S P ++N +      L L  T+
Sbjct:   143 ---NGNLKSSSSSSKQSSSVNAQSPSSGQLRTNHQFPFS-PTLYNLTQLGGIGLNLAATN 198

Query:   208 QNPNINPTGPSTSTSSV 224
              N   +  G S   S +
Sbjct:   199 GNNQAHQIGSSLMMSDL 215

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

 Score = 272 (100.8 bits), Expect = 4.0e-26, Sum P(2) = 4.0e-26
 Identities = 46/61 (75%), Positives = 51/61 (83%)

Query:    86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKN-KSSS 144
             + L CPRCDSSNTKFCYYNNYN +QPRHFCK CRRYWT GG LR+VP+GGG RK+ K S 
Sbjct:    28 EQLPCPRCDSSNTKFCYYNNYNFSQPRHFCKACRRYWTHGGTLRDVPVGGGTRKSAKRSR 87

Query:   145 T 145
             T
Sbjct:    88 T 88

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

---

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: GSVIVG00003895001 SubName- Full=Chromosome undetermined scaffold_560, whole genome shotgun sequence; Flags- Fragment; (226 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	366
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	1e-38

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

 Score =  131 bits (332), Expect = 1e-38
 Identities = 48/60 (80%), Positives = 53/60 (88%)

Query: 86  QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSST 145
           + L+CPRCDS NTKFCYYNNYNL QPR+FCK CRRYWT GGALRNVP+GGG RKNK SS+
Sbjct: 4   KALKCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKRSSS 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	366
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	93.41
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	93.2
COG3677	129	Transposase and inactivated derivatives [DNA repli	92.77
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	91.02
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	89.1
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	85.76
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	84.22

>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=8.1e-37  Score=235.43  Aligned_cols=61  Identities=80%  Similarity=1.580  Sum_probs=59.3

Q ss_pred             CCCCcCCCCCCCCCceeeeecCcCCCCCcccccccccccccCcccccccCCCCcccCCCCC
Q 040161           84 NNQNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTKGGALRNVPIGGGCRKNKSSS  144 (366)
Q Consensus        84 ~~e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~GGtLRNVPVGGG~RKnK~ss  144 (366)
                      +++.++||||+|.||||||||||++.||||||++|+||||+||+|||||||||+||+|+++
T Consensus         2 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg~Rk~k~~~   62 (63)
T PF02701_consen    2 PEQPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGGCRKNKRSS   62 (63)
T ss_pred             CccCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCCcccCCcCC
Confidence            5688999999999999999999999999999999999999999999999999999999987

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent

>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit

Probab=93.41  E-value=0.032  Score=48.79  Aligned_cols=34  Identities=24%  Similarity=0.728  Sum_probs=27.3

Q ss_pred             CcCCCCCCCCCceeeeecCc--CCCCCccccccccccc
Q 040161           87 NLRCPRCDSSNTKFCYYNNY--NLTQPRHFCKTCRRYW  122 (366)
Q Consensus        87 ~~~CPRC~S~nTKFcYYNNy--n~~QPRhfCksCrRYW  122 (366)
                      ...||||.|.+|+..  +.|  +.++.-|+|++|+.=+
T Consensus       105 ~~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf  140 (146)
T TIGR02159       105 SVQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPF  140 (146)
T ss_pred             CCcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcH
Confidence            589999999999964  566  4457779999998644

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

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

Probab=93.20  E-value=0.079  Score=37.77  Aligned_cols=29  Identities=34%  Similarity=0.825  Sum_probs=23.3

Q ss_pred             CCcCCCCCCCCCceeeeecCcCCCCCccccccccc
Q 040161           86 QNLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRR  120 (366)
Q Consensus        86 e~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrR  120 (366)
                      ++..||+|.+.  ++..+.+    +.+|.|++|++
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            34779999998  6666665    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=92.77  E-value=0.074  Score=45.65  Aligned_cols=36  Identities=33%  Similarity=0.653  Sum_probs=28.5

Q ss_pred             CcCCCCCCCCCceeeeecCcCCCCCccccccccccccc
Q 040161           87 NLRCPRCDSSNTKFCYYNNYNLTQPRHFCKTCRRYWTK  124 (366)
Q Consensus        87 ~~~CPRC~S~nTKFcYYNNyn~~QPRhfCksCrRYWT~  124 (366)
                      ...||+|.+.+  +-=+.-+.....||.|++|++-|+.
T Consensus        30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~   65 (129)
T COG3677          30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV   65 (129)
T ss_pred             cCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence            47899999999  3335555555999999999999874

>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=91.02  E-value=0.15  Score=35.98  Aligned_cols=31  Identities=35%  Similarity=0.790  Sum_probs=21.6

Q ss_pred             CcCCCCCCCCCceeeeecCcCCC-CCcccccccc
Q 040161           87 NLRCPRCDSSNTKFCYYNNYNLT-QPRHFCKTCR  119 (366)
Q Consensus        87 ~~~CPRC~S~nTKFcYYNNyn~~-QPRhfCksCr  119 (366)
                      .+.||||.+.+.  -|=|-.+.. ..||+|++|+
T Consensus         5 ~v~CP~C~s~~~--v~k~G~~~~G~qryrC~~C~   36 (36)
T PF03811_consen    5 DVHCPRCQSTEG--VKKNGKSPSGHQRYRCKDCR   36 (36)
T ss_pred             eeeCCCCCCCCc--ceeCCCCCCCCEeEecCcCC
Confidence            368999999872  123444333 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=89.10  E-value=0.42  Score=33.83  Aligned_cols=37  Identities=22%  Similarity=0.697  Sum_probs=27.9

Q ss_pred             cCCCCCCCCCceeeeecCcCCCCC---ccccccccccccc
Q 040161           88 LRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWTK  124 (366)
Q Consensus        88 ~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT~  124 (366)
                      .+||+|...+.-|-..+-.....|   -|.|.+|...|..
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            379999977777666655655555   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=85.76  E-value=0.66  Score=32.61  Aligned_cols=35  Identities=23%  Similarity=0.738  Sum_probs=24.0

Q ss_pred             CCCCCCCCCceeeeecCcCCCCCc---ccccccccccc
Q 040161           89 RCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWT  123 (366)
Q Consensus        89 ~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT  123 (366)
                      +||+|...+..|--.+......|-   |.|.+|..-|+
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            799999988766555555555443   99999999995

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=84.22  E-value=0.51  Score=44.10  Aligned_cols=38  Identities=21%  Similarity=0.647  Sum_probs=18.8

Q ss_pred             CCcCCCCCCCCC-ceeeeecCcCCC-CCcccccccccccc
Q 040161           86 QNLRCPRCDSSN-TKFCYYNNYNLT-QPRHFCKTCRRYWT  123 (366)
Q Consensus        86 e~~~CPRC~S~n-TKFcYYNNyn~~-QPRhfCksCrRYWT  123 (366)
                      ....||.|...+ .++-||..-... .--+.|+.|+.|+-
T Consensus       210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK  249 (290)
T PF04216_consen  210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK  249 (290)
T ss_dssp             -TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred             cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence            467899999854 567777433333 33499999999983

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.

---

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	366
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	84.12
1tfi_A	50	Transcriptional elongation factor SII; transcripti	81.29

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

Probab=84.12  E-value=0.85  Score=32.52  Aligned_cols=38  Identities=18%  Similarity=0.590  Sum_probs=25.8

Q ss_pred             CcCCCCCCCCCceeeeecCcCCCCC---ccccccccccccc
Q 040161           87 NLRCPRCDSSNTKFCYYNNYNLTQP---RHFCKTCRRYWTK  124 (366)
Q Consensus        87 ~~~CPRC~S~nTKFcYYNNyn~~QP---RhfCksCrRYWT~  124 (366)
                      ..+||+|...+..|--.+-.....|   .|.|..|.--|..
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            5789999984444433333333444   3999999999976

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

Probab=81.29  E-value=1.1  Score=32.09  Aligned_cols=38  Identities=18%  Similarity=0.614  Sum_probs=28.4

Q ss_pred             CCcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccc
Q 040161           86 QNLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWT  123 (366)
Q Consensus        86 e~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT  123 (366)
                      ....||+|...+..|--.+..+...|-   |.|..|..-|.
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            347899999887776665555555553   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	366
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	93.41
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	88.75
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	83.52

>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=93.41  E-value=0.068  Score=39.70  Aligned_cols=41  Identities=20%  Similarity=0.504  Sum_probs=31.3

Q ss_pred             CcCCCCCCCCCceeeeecCcCCCCCc---ccccccccccccCcc
Q 040161           87 NLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWTKGGA  127 (366)
Q Consensus        87 ~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT~GGt  127 (366)
                      ...||+|...+.-|-+.+-....-|-   |.|..|.-.|+...+
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            47899999887777666665554443   899999999998543

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

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

Probab=88.75  E-value=0.14  Score=35.73  Aligned_cols=37  Identities=19%  Similarity=0.630  Sum_probs=31.0

Q ss_pred             CCcCCCCCCCCCceeeeecCcCCCCCc---cccccccccc
Q 040161           86 QNLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYW  122 (366)
Q Consensus        86 e~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYW  122 (366)
                      ...+||+|.+.+..|--++..+...|-   +.|..|..-|
T Consensus         8 ~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~W   47 (50)
T d1tfia_           8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRW   47 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEE
T ss_pred             CCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCee
Confidence            458999999998887777777777765   8999999988

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

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

Probab=83.52  E-value=0.42  Score=33.79  Aligned_cols=38  Identities=18%  Similarity=0.616  Sum_probs=28.9

Q ss_pred             CcCCCCCCCCCceeeeecCcCCCCCc---cccccccccccc
Q 040161           87 NLRCPRCDSSNTKFCYYNNYNLTQPR---HFCKTCRRYWTK  124 (366)
Q Consensus        87 ~~~CPRC~S~nTKFcYYNNyn~~QPR---hfCksCrRYWT~  124 (366)
                      ...||+|...+.-|--.+-....-|-   |.|..|+.-|..
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            47899999888777666655555544   899999999963