Citrus Sinensis ID: 042156

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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------
Protein Sequence
MQQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSPPHPNLTTTQQNILSSSNPVITTGPPVLRTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKIYHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNNPNVPDHDTSLWSISTASANSNNTNTASVSGSLNPNQWRDLPGYGPPP
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccHHHccccccccccccccccccccEEEEEcccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mqqqerggsseeRKQQDRRLKTmqggtenqqqqeqpqpqkcprceslntkfcyynnyslsqpryfcKTCRrywtqggtlrnvpvgggcrkgkrtktssvsgeasrasqppqppspphpnltttqqnilsssnpvittgppvlrtklepaaaspsmgsyypsggflSSLAAIqsqsfnpqplhqafnvggadhhhniggssnldllqgfstvpsfgsshtqhQQIQQSKIYhhqmgnidksanpmhmmyhtipsdqenltiqsrrpgsstshhqqhdwhqqgsfinnsnnpnvpdhdtsLWSISTasansnntntasvsgslnpnqwrdlpgygppp
Flexible Loop (DISEMBL)
mqqqerggsseerkqqdRRLKTMqggtenqqqqeqpqpqkcPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWtqggtlrnvpvgggcrkgkrtktssvsgeasrasqppqppspphPNLTTTQQNILSSSNPVITTGPPVLRTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKIYHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNNPNVPDHDTSLWSISTASANSNNTNtasvsgslnpnqwrdlpgygppp
Low Complexity Region (SEG)
MQQQERGGSSEERKQQDRRLKTMqggtenqqqqeqpqpqKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVgggcrkgkrtktSSVSGEASRAsqppqppspphpNLTTTQQNILSSSNPVITTGPPVLRTKLEpaaaspsmgsyypsggFLSSLAAIQSQSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGsshtqhqqiqqskiyhhqMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNNPNVPDHDTSLWSIstasansnntntasVSGSLNPNQWRDLPGYGPPP
Disordered region (IsUnstruct)
*******************************************CESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGG*************************************************************************************************FNVG**************DLLQ**********************************************************************************************************************************
Disordered Region (DISOPRED)
*****************************************PRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNV************************************************************************************************************************************************************************************************************************LWSISTASAN***********SLNPNQWRDLPGYG***
Disordered Region (DISEMBL)
****************************************CPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGG********************************LTTTQQNILSSSNPVITTGPPVLRTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVP****************IYHHQMGNIDKSANPMHMMYHTIPSDQENLTIQ*****************QQGSFINNSNNPNVPDHDTSLWSISTASANSNNTNTASVSGSLNPNQWRDLPGYGPPP
Disordered Region (DISPRO)
***********************************PQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG*********************************************SNPVITTGPPVLRTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFN*********VGG**HHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKIYHHQMGNIDKSANPMHMMYHTIPSDQ*******************************************************************PNQWRDLPGYGP**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSPPHPNLTTTQQNILSSSNPVITTGPPVLRTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKIYHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNNPNVPDHDTSLWSISTASANSNNTNTASVSGSLNPNQWRDLPGYGPPP
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	336	2.2.26 [Sep-21-2011]
Q8LDR0	307	Dof zinc finger protein D	yes	no	0.232	0.254	0.674	4e-28
O24463	328	Dof zinc finger protein P	N/A	no	0.336	0.344	0.504	1e-27
Q84TE9	257	Dof zinc finger protein D	no	no	0.339	0.443	0.491	8e-27
Q8LE43	288	Dof zinc finger protein D	no	no	0.187	0.218	0.793	1e-26
O80928	330	Dof zinc finger protein D	no	no	0.166	0.169	0.839	5e-26
Q9FM03	372	Dof zinc finger protein D	no	no	0.154	0.139	0.923	6e-26
Q43385	296	Dof zinc finger protein D	no	no	0.485	0.550	0.415	3e-25
Q8LAP8	342	Dof zinc finger protein D	no	no	0.202	0.198	0.705	6e-25
Q9SVC5	247	Dof zinc finger protein D	no	no	0.172	0.234	0.827	7e-25
P68349	260	Dof zinc finger protein D	no	no	0.199	0.257	0.716	2e-24

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

 Score =  125 bits (315), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 56/83 (67%), Positives = 62/83 (74%), Gaps = 5/83 (6%)

Query: 17  DRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQG 76
           DRR++  Q    N  Q       KCPRC SLNTKFCYYNNY+LSQPR+FCK CRRYWT+G
Sbjct: 34  DRRMRAHQNNILNHHQ-----SLKCPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKG 88

Query: 77  GTLRNVPVGGGCRKGKRTKTSSV 99
           G LRNVPVGGGCRK KR+KT  V
Sbjct: 89  GVLRNVPVGGGCRKAKRSKTKQV 111

Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. Enhances the DNA binding of OBF transcription factors to OCS elements.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  124 bits (310), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 57/113 (50%), Positives = 73/113 (64%)

Query: 15  QQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWT 74
           +Q R +  + G  E + + + P+  KCPRC+S NTKFCYYNNYS+SQPRYFCK CRRYWT
Sbjct: 36  KQTRAMPQIGGSGERKPRPQLPEALKCPRCDSNNTKFCYYNNYSMSQPRYFCKACRRYWT 95

Query: 75  QGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSPPHPNLTTTQQNI 127
            GGTLRNVP+GGGCRK K      +    S +S     P  P  N +++  +I
Sbjct: 96  HGGTLRNVPIGGGCRKNKHASRFVLGSHTSSSSSATYAPLSPSTNASSSNMSI 148

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

 Score =  121 bits (303), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 60/122 (49%), Positives = 78/122 (63%), Gaps = 8/122 (6%)

Query: 35  QPQP----QKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRK 90
           +PQP     +CPRC+S NTKFCYYNNYSL+QPRYFCK+CRRYWT+GGTLRN+PVGGGCRK
Sbjct: 47  RPQPPELALRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPVGGGCRK 106

Query: 91  GKRTKTSSVSGEASRASQPPQPPSPPHPNLTTTQQNILSSSNPVITTGPPVLRTKLEPAA 150
            KR+ +S+    A      P+P S      +    N  S++  +  +    L  K  P +
Sbjct: 107 NKRSTSSA----ARSLRTTPEPASHDGKVFSAAGFNGYSNNEHIDLSLAFALLNKQHPGS 162

Query: 151 AS 152
           +S
Sbjct: 163 SS 164

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LE43|DOF21_ARATH Dof zinc finger protein DOF2.1 OS=Arabidopsis thaliana GN=DOF2.1 PE=2 SV=2

 Score =  120 bits (302), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 57/63 (90%)

Query: 37  QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKT 96
           + Q CPRCES NTKFCYYNNYSLSQPRYFCK+CRRYWT+GGTLRNVPVGGGCR+ KR+ +
Sbjct: 46  EAQNCPRCESPNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPVGGGCRRNKRSSS 105

Query: 97  SSV 99
           S+ 
Sbjct: 106 SAF 108

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 =  118 bits (296), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 47/56 (83%), Positives = 53/56 (94%)

Query: 40  KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTK 95
           KCPRCES NTKFCY+NNYSL+QPR+FCKTCRRYWT+GG LRNVPVGGGCR+ +RTK
Sbjct: 90  KCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNRRTK 145

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FM03|DOF56_ARATH Dof zinc finger protein DOF5.6 OS=Arabidopsis thaliana GN=DOF5.6 PE=2 SV=2

 Score =  118 bits (296), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 48/52 (92%), Positives = 51/52 (98%)

Query: 38  PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCR 89
           PQKCPRCES +TKFCYYNNYSLSQPRYFCKTCRRYWT+GGTLRN+PVGGGCR
Sbjct: 72  PQKCPRCESTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPVGGGCR 123

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  115 bits (289), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 74/178 (41%), Positives = 95/178 (53%), Gaps = 15/178 (8%)

Query: 30  QQQQEQPQPQ-KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGC 88
           + ++ +PQ +  CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWT+GG+LRNVPVGG  
Sbjct: 64  ETRKARPQEKVNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGSS 123

Query: 89  RKGKRTKT--SSVSGEASRASQPPQPPSPPHPNLTTTQQNILSSSNPVITT----GPPVL 142
           RK KR+ T  +S S        PP   S   PN +    N+LS   PV+         +L
Sbjct: 124 RKNKRSSTPLASPSNPKLPDLNPPILFSSQIPNKSNKDLNLLSF--PVMQDHHHHALELL 181

Query: 143 RTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFNPQPLHQAFNVG---GADHHHNIG 197
           R+      +S  M ++ P     S+     S  F   P ++  N       DHH  IG
Sbjct: 182 RSN---GVSSRGMNTFLPGQMMDSNSVLYSSLGFPTMPDYKQSNNNLSFSIDHHQGIG 236

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LAP8|DOF46_ARATH Dof zinc finger protein DOF4.6 OS=Arabidopsis thaliana GN=DOF4.6 PE=2 SV=2

 Score =  115 bits (287), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 48/68 (70%), Positives = 55/68 (80%)

Query: 26  GTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85
           G E + + E+ Q   CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWT+GG+LRN+PVG
Sbjct: 40  GGERKARPEKDQAVNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNIPVG 99

Query: 86  GGCRKGKR 93
           GG RK KR
Sbjct: 100 GGSRKNKR 107

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVC5|DOF35_ARATH Dof zinc finger protein DOF3.5 OS=Arabidopsis thaliana GN=DOF3.5 PE=3 SV=1

 Score =  115 bits (287), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 48/58 (82%), Positives = 53/58 (91%)

Query: 41 CPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSS 98
          CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWT+GG+LRNVPVGGGCRK +R K+SS
Sbjct: 27 CPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKSRRPKSSS 84

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

Arabidopsis thaliana (taxid: 3702)

>sp|P68349|DOF12_ARATH Dof zinc finger protein DOF1.2 OS=Arabidopsis thaliana GN=DOF1.2 PE=2 SV=1

 Score =  113 bits (283), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/67 (71%), Positives = 55/67 (82%)

Query: 32 QQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKG 91
          +QE      CPRC S NTKFCYYNNYSLSQPRYFCK CRRYWT+GG+LRN+PVGGGCRK 
Sbjct: 31 EQEAITAPACPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNIPVGGGCRKR 90

Query: 92 KRTKTSS 98
           R++ +S
Sbjct: 91 SRSRQNS 97

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	336
224079181	325	f-box family protein [Populus trichocarp	0.895	0.926	0.539	7e-73
224125372	325	f-box family protein [Populus trichocarp	0.901	0.932	0.517	1e-64
147768311	299	hypothetical protein VITISV_041540 [Viti	0.848	0.953	0.478	2e-51
225443642	299	PREDICTED: uncharacterized protein LOC10	0.848	0.953	0.478	2e-51
356557701	313	PREDICTED: uncharacterized protein LOC10	0.913	0.980	0.421	5e-49
255536775	314	zinc finger protein, putative [Ricinus c	0.818	0.875	0.446	1e-45
351726006	327	Dof9 [Glycine max] gi|112363372|gb|ABI16	0.779	0.801	0.365	4e-29
449434340	238	PREDICTED: dof zinc finger protein DOF5.	0.345	0.487	0.596	6e-29
113205234	299	Dof domain, zinc finger family protein [	0.321	0.361	0.544	2e-28
357446657	336	Dof zinc finger protein-like protein [Me	0.196	0.196	0.818	5e-28

>gi|224079181|ref|XP_002305784.1| f-box family protein [Populus trichocarpa] gi|222848748|gb|EEE86295.1| f-box family protein [Populus trichocarpa]

 Score =  280 bits (716), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 193/358 (53%), Positives = 227/358 (63%), Gaps = 57/358 (15%)

Query: 1   MQQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLS 60
           MQ++ +GGS + +  Q+RRLK+ QG        +Q QPQKCPRCESLNTKFCYYNNYSLS
Sbjct: 1   MQRKMQGGSEDVKPNQERRLKSTQG-------DDQQQPQKCPRCESLNTKFCYYNNYSLS 53

Query: 61  QPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKT-SSVSGEASRASQPPQPPSPPHPN 119
           QPRYFCKTC+RYWT GGT+RNVPVGGGCRKGKR KT SS SGE SR  Q  Q  S    +
Sbjct: 54  QPRYFCKTCKRYWTLGGTMRNVPVGGGCRKGKRAKTSSSSSGENSRLQQQLQQQSQLLQH 113

Query: 120 LTTTQQNILSSSNPVITTGPPVLRTKLEPAAASP------SMGSYYPSGGFLSSLAAIQS 173
              T QNIL+++N   +   P LRTK      SP      SMGSY+P  GFL+SL AIQS
Sbjct: 114 NLATPQNILATTNSGNSVS-PALRTKESGNLVSPPTPGMSSMGSYFPGDGFLTSLEAIQS 172

Query: 174 --------QSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQ 225
                   QSF+ QPL+Q  N+GG     ++G +SNL LL GFS VP+FGS     Q  Q
Sbjct: 173 LNNNQPPIQSFSFQPLNQPVNLGG-----DLGDTSNLGLLHGFSAVPAFGS-----QNQQ 222

Query: 226 QSKIYHHQMGNIDKSANP--MHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSF 283
           Q + YH     +D   N    H  Y   P DQE+L IQS RP ++TS HQQ +WHQ   F
Sbjct: 223 QRQFYH-----VDNRGNKSVEHSFY---PHDQESL-IQSSRP-AATSSHQQQNWHQ--GF 270

Query: 284 INNSNNPNVPDHDTSLWSISTASA----NSN-NTNTASVSGSLNPNQW-RDLPGYGPP 335
           I+NS NP V   D  LWSIST++     NSN NT TA  S SLNP+QW  DLPG GPP
Sbjct: 271 ISNS-NPTV--SDAVLWSISTSTTIGHPNSNINTGTAG-SASLNPDQWHHDLPGNGPP 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125372|ref|XP_002329789.1| f-box family protein [Populus trichocarpa] gi|222870851|gb|EEF07982.1| f-box family protein [Populus trichocarpa]

 Score =  253 bits (645), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 181/350 (51%), Positives = 223/350 (63%), Gaps = 47/350 (13%)

Query: 6   RGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYF 65
           +GGS + +  Q+RRLK+ Q   ++QQQ +  QPQKCPRCESLNTKFCYYNNY+LSQPRYF
Sbjct: 2   QGGSEDVKPNQERRLKSTQ--GDDQQQHQPQQPQKCPRCESLNTKFCYYNNYNLSQPRYF 59

Query: 66  CKTCRRYWTQGGTLRNVPVGGGCRKGKRTKT--SSVSGEASRASQPPQPPSPPHPNLTTT 123
           CKTCRRYWT GGTLRNVPVGGGCRKGKR KT  SS SGE SR  Q          +   T
Sbjct: 60  CKTCRRYWTLGGTLRNVPVGGGCRKGKRAKTSSSSSSGENSRLQQQLPQQPHLLQHNFAT 119

Query: 124 QQNILSSSNPVITTGPPVLRTK------LEPAAASPSMGSYYPSGGFLSSLAAIQS---- 173
            QNIL+++N    +  P LR K      L PA    +MGSY+P GGF +SL AIQS    
Sbjct: 120 PQNILATNNSGNLSS-PALRNKESGNLVLPPAPGMSTMGSYFPGGGFFTSLEAIQSLNNN 178

Query: 174 ----QSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKI 229
               QSF  QPL+Q  N+GG      +G +SNL LL GF+ VP+FGS     Q  QQS+ 
Sbjct: 179 QPPIQSFPLQPLNQPVNLGGV-----LGETSNLGLLHGFNAVPAFGS-----QNQQQSQF 228

Query: 230 YHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNN 289
           YH  +G  D + +  H  Y   P +QE+L IQS RP  +TS HQQ +WH    F++NS +
Sbjct: 229 YH--VGYRD-TRSIEHSFY---PHNQESL-IQSSRP--ATSSHQQQNWHH--GFMSNS-S 276

Query: 290 PNVPDHDTSLWSISTASA---NSNNTNTASVSGSLNPNQWR-DLPGYGPP 335
           P V   DT+LWS ST++     ++N N  + S  LNP+QW+ DLPGYGPP
Sbjct: 277 PTV--SDTALWSTSTSTTIGHTNSNINPTAGSSPLNPDQWKHDLPGYGPP 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147768311|emb|CAN78117.1| hypothetical protein VITISV_041540 [Vitis vinifera]

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 166/347 (47%), Positives = 202/347 (58%), Gaps = 62/347 (17%)

Query: 2   QQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQ 61
           Q +++GG  E+    DRRLK  Q  +ENQQQQ    PQKCPRC+S+NTKFCYYNNYSLSQ
Sbjct: 3   QDRDKGGGXEDVDPPDRRLKPAQ--SENQQQQ---LPQKCPRCDSINTKFCYYNNYSLSQ 57

Query: 62  PRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSPPHPNLT 121
           PRYFCKTCRRYWTQGGTLRNVPVGGGCRK KR    S SG+ SR+     P      NL 
Sbjct: 58  PRYFCKTCRRYWTQGGTLRNVPVGGGCRKTKRKP--SASGDNSRSQ---LPTQQQQQNLA 112

Query: 122 TTQQNILSSSNPVITTGPPVLRTKLEPA-----------AASPSMGSYYPSGGFLSSLAA 170
               NI+S+++ V     P LR   EPA               S+  YYP+G FLSSL A
Sbjct: 113 APPPNIISTNSGVAVG--PALRIA-EPANLSPAPAPASAPTLSSVNPYYPAGAFLSSLPA 169

Query: 171 IQS-QSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKI 229
           ++      PQP +Q  NVG      + GG SNL +LQGF+ VPS GS   Q QQ +    
Sbjct: 170 MRPLNQPQPQPFNQPVNVG-----RDFGG-SNLAILQGFN-VPSLGSQQQQRQQAE---- 218

Query: 230 YHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNN 289
             +QMGN D++   ++          E+L IQS RP   T H  Q++WHQ  +FI    N
Sbjct: 219 -FYQMGNRDRNIESLY-------GSGEDL-IQSSRP---TGH--QNNWHQ--TFI----N 258

Query: 290 PNVPDHDTSLWSISTASANSNNTNTASVSGSLNPNQWRDLPGYGPPP 336
           P  P  D++LWSI      S+N N+ + S S N N W DL GYGPPP
Sbjct: 259 PTAP--DSNLWSI----GGSSNNNSNAASSSFNQNHWADLQGYGPPP 299

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443642|ref|XP_002274050.1| PREDICTED: uncharacterized protein LOC100246919 [Vitis vinifera] gi|297740407|emb|CBI30589.3| unnamed protein product [Vitis vinifera]

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 166/347 (47%), Positives = 202/347 (58%), Gaps = 62/347 (17%)

Query: 2   QQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQ 61
           Q +++GG  E+    DRRLK  Q  +ENQQQQ    PQKCPRC+S+NTKFCYYNNYSLSQ
Sbjct: 3   QDRDKGGGLEDVDPPDRRLKPAQ--SENQQQQ---LPQKCPRCDSINTKFCYYNNYSLSQ 57

Query: 62  PRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSPPHPNLT 121
           PRYFCKTCRRYWTQGGTLRNVPVGGGCRK KR    S SG+ SR+     P      NL 
Sbjct: 58  PRYFCKTCRRYWTQGGTLRNVPVGGGCRKTKRKP--SASGDNSRSQ---LPTQQQQQNLA 112

Query: 122 TTQQNILSSSNPVITTGPPVLRTKLEPA-----------AASPSMGSYYPSGGFLSSLAA 170
               NI+S+++ V     P LR   EPA               S+  YYP+G FLSSL A
Sbjct: 113 APPPNIISTNSGVAVG--PALRIA-EPANLSPAPAPASAPTLSSVNPYYPAGAFLSSLPA 169

Query: 171 IQS-QSFNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKI 229
           ++      PQP +Q  NVG      + GG SNL +LQGF+ VPS GS   Q QQ +    
Sbjct: 170 MRPLNQPQPQPFNQPVNVG-----RDFGG-SNLAILQGFN-VPSLGSQQQQRQQAE---- 218

Query: 230 YHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNN 289
             +QMGN D++   ++          E+L IQS RP   T H  Q++WHQ  +FI    N
Sbjct: 219 -FYQMGNRDRNIESLY-------GSGEDL-IQSSRP---TGH--QNNWHQ--TFI----N 258

Query: 290 PNVPDHDTSLWSISTASANSNNTNTASVSGSLNPNQWRDLPGYGPPP 336
           P  P  D++LWSI      S+N N+ + S S N N W DL GYGPPP
Sbjct: 259 PTAP--DSNLWSI----GGSSNNNSNAASSSFNQNHWADLQGYGPPP 299

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557701|ref|XP_003547152.1| PREDICTED: uncharacterized protein LOC100817065 [Glycine max]

 Score =  201 bits (510), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 144/342 (42%), Positives = 186/342 (54%), Gaps = 35/342 (10%)

Query: 1   MQQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLS 60
           M+Q    G    +  +D R+K ++ G    Q Q   QPQKCPRC+SLNTKFCYYNNYSLS
Sbjct: 1   MEQGVEEGGGMNKIPRDSRVKEIRQGDAQIQVQAPQQPQKCPRCDSLNTKFCYYNNYSLS 60

Query: 61  QPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSPPHPNL 120
           QPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKR K+S+ S   +  S     P       
Sbjct: 61  QPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRAKSSNSSSSENMNSSSRSLPQ----QQ 116

Query: 121 TTTQQNILSSSNPVITTGPPVLRTKLEPAAASPSMGSYYPSGGFLSSLAAIQSQSFNPQP 180
              Q  ++ +  P +TT   V++ K +P++   S  ++Y SGG+LSSLAA+ S + +  P
Sbjct: 117 QQPQGVVVQTQAPPLTT---VVKAK-DPSSVVAS--TFYQSGGYLSSLAAMHSLNSSSHP 170

Query: 181 LHQAFNVGGADHHHNIGGSSNLDLLQGFSTVPSFGSSHTQHQQIQQSKIYHHQMGNIDKS 240
              + N  G+D       SSNL LL GF+     G     H         +HQMG+ ++ 
Sbjct: 171 FDHSLNFAGSDTLR----SSNLGLLSGFNVQRPIGPIRPPH--------LYHQMGSGERE 218

Query: 241 ANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFI-NNSNNPNVPDHDTSL 299
              ++      PS        +   G S     QHDW    SFI NN+NN +    D SL
Sbjct: 219 MVSLYEQGLVNPSSSSMANTDTNSSGVS-----QHDWPM--SFINNNNNNASNRASDASL 271

Query: 300 WSI--STASANSNNTNTASV---SGSLNPNQWRDLPGYGPPP 336
           WS   +T   N+  T+ + V   S S   NQW +LPGYGPPP
Sbjct: 272 WSTISTTVGGNAERTSPSGVGAGSSSFVKNQWPNLPGYGPPP 313

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255536775|ref|XP_002509454.1| zinc finger protein, putative [Ricinus communis] gi|223549353|gb|EEF50841.1| zinc finger protein, putative [Ricinus communis]

 Score =  189 bits (481), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 156/349 (44%), Positives = 201/349 (57%), Gaps = 74/349 (21%)

Query: 16  QDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQ 75
           QDRR++         Q Q Q QPQKCPRCES+NTKFCYYNNYSLSQPRYFCKTCRRYWTQ
Sbjct: 12  QDRRIQ------GENQNQPQQQPQKCPRCESMNTKFCYYNNYSLSQPRYFCKTCRRYWTQ 65

Query: 76  GGTLRNVPVGGGCRKGKRTK--TSSVSGEASRASQPPQPPSPPHPNLTTTQQNILSSSNP 133
           GGTLRNVPVGGGCRKGKR K  +SS S  ++  +      +    +L  T QN+++S++ 
Sbjct: 66  GGTLRNVPVGGGCRKGKRVKTSSSSSSASSTTTTSSSSSENSRSQSLANTTQNMITSTS- 124

Query: 134 VITTGPPVLRTK----LEPAAASPSMGSY-YPS----GGFL-SSLAAIQS--------QS 175
            ++ G   LR K    L     + S+G+Y Y S    GGFL +SLAAIQS        QS
Sbjct: 125 -VSLG---LRAKESGNLVSTPGASSVGTYNYSSAGGGGGFLMNSLAAIQSLSNQPTLPQS 180

Query: 176 FNPQPLHQAFNVGGADHHHNIGGSSNLDLLQGF-STVPSFGSSHTQHQQIQQSKIYHHQM 234
           F+    HQ  N+GG       GG S+L LL GF + VPSFGS   Q Q+        + M
Sbjct: 181 FSLN--HQPVNLGG----DFAGGGSSLSLLHGFNAVVPSFGSQQIQQQRQ------FYNM 228

Query: 235 GNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSSTSHHQQHDWHQQGSFINNSNNP-NVP 293
           G+ D      H  Y                  ++++HHQQ    Q   FI ++ NP NV 
Sbjct: 229 GSRDNRNTGDHPFY-----------------AAASAHHQQ----QTAGFITSNTNPTNVS 267

Query: 294 DHDTSLWSISTASANSNNTNTASV----SGSLNP-NQW-RDLPGYGPPP 336
             DT+LWS+ST++A  N ++++++    S +LNP +QW   LPGYGPPP
Sbjct: 268 --DTALWSVSTSTAAGNTSSSSNIVNGGSFTLNPTDQWLHHLPGYGPPP 314

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726006|ref|NP_001236600.1| Dof9 [Glycine max] gi|112363372|gb|ABI16010.1| Dof9 [Glycine max]

 Score =  135 bits (339), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 115/315 (36%), Positives = 156/315 (49%), Gaps = 53/315 (16%)

Query: 40  KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSV 99
           KCPRC+S+NTKFCY+NNYSLSQPR+FCK C+RYWT GGT RN+PVGGG RK KR KT+S 
Sbjct: 46  KCPRCDSMNTKFCYFNNYSLSQPRHFCKACKRYWTLGGTFRNIPVGGGSRKVKRGKTNSP 105

Query: 100 SGEASRASQPPQPPSPPHPNLTTTQQNILSSSNPVITTGPPVLRTKLEPAAASPSMGSYY 159
           S  +S +S       P        QQN+L      +   PP L T     + SP    YY
Sbjct: 106 SSSSSSSSCSNLLSQP--------QQNLL------MRPSPPPLTTNTMVQSTSP---YYY 148

Query: 160 PSG----GFLSSLAAIQSQSFNPQPLHQAFNVGGADHHHNIGGSSNLD-LLQGFSTVPSF 214
             G    G+LS  +++ + + + QP  Q   VGG DH   + GSSN+  L+ GF+   S+
Sbjct: 149 NLGVGGNGYLSFHSSLNNNTPS-QPSDQYLKVGGGDH---VAGSSNISPLVSGFNNAASY 204

Query: 215 G-----SSHTQHQQIQQSKIYHHQMGNIDKSANPMHMMYHTIPSDQENLTIQSRRPGSST 269
                     Q Q +  ++    ++ NI     P +M   +       +  QS     ST
Sbjct: 205 SLPPRFHHQQQQQSMHPAQRQQQRLINI-----PSNMASSSSDVSHSGVRPQSLINNVST 259

Query: 270 SHHQQHDWHQQGSFINNSNNPNVPDHDTSLWSISTASANS---NNTNTASVSG------S 320
           S           +   ++N+  +   D SLWS +T +A S   N+     V G      S
Sbjct: 260 STDH--------NVSTSTNHRAITTSDASLWSAATINATSIGGNSDQNNVVKGSSSSSSS 311

Query: 321 LNPNQWRDLPGYGPP 335
           L PN W   PG+GPP
Sbjct: 312 LVPNLWVHRPGFGPP 326

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434340|ref|XP_004134954.1| PREDICTED: dof zinc finger protein DOF5.8-like [Cucumis sativus] gi|449479597|ref|XP_004155647.1| PREDICTED: dof zinc finger protein DOF5.8-like [Cucumis sativus]

 Score =  134 bits (337), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 77/129 (59%), Positives = 86/129 (66%), Gaps = 13/129 (10%)

Query: 16  QDRRLKTMQGGTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQ 75
           QDRRLK++Q   + Q Q +     KCPRC+SLNTKFCYYNNYSLSQPRY CKTCRRYWT 
Sbjct: 4   QDRRLKSVQVQDQVQPQPQ-----KCPRCDSLNTKFCYYNNYSLSQPRYLCKTCRRYWTH 58

Query: 76  GGTLRNVPVGGGCRKGKRTKTSSVSGEA--------SRASQPPQPPSPPHPNLTTTQQNI 127
           GGTLRNVPVGGGCRKGKR K  S S           + AS  P P   P    TTT Q++
Sbjct: 59  GGTLRNVPVGGGCRKGKRLKQPSQSSNNSSVKPLVQTSASPLPPPQIVPLSLSTTTSQHV 118

Query: 128 LSSSNPVIT 136
           + S  PVIT
Sbjct: 119 IYSGTPVIT 127

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|113205234|gb|AAT39305.2| Dof domain, zinc finger family protein [Solanum demissum]

 Score =  132 bits (332), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 67/123 (54%), Positives = 86/123 (69%), Gaps = 15/123 (12%)

Query: 1   MQQQERGGSSEERKQQDRRLKTMQGGTENQQQQEQP-----QPQKCPRCESLNTKFCYYN 55
           M QQ++  SS+        L++M   T+  Q Q++P     QPQKCPRC+S NTKFCYYN
Sbjct: 1   MDQQQQEMSSQT-------LESMLVCTKPDQDQKKPRPAEQQPQKCPRCDSANTKFCYYN 53

Query: 56  NYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKTSSVSGEASRASQPPQPPSP 115
           NYSL+QPRYFCK+CRRYWT+GGTLRNVPVGGGCRK K+  +++    A R+SQ    P+ 
Sbjct: 54  NYSLTQPRYFCKSCRRYWTKGGTLRNVPVGGGCRKNKKLSSTT---SAKRSSQDNISPNI 110

Query: 116 PHP 118
            +P
Sbjct: 111 SNP 113

Source: Solanum demissum

Species: Solanum demissum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446657|ref|XP_003593604.1| Dof zinc finger protein-like protein [Medicago truncatula] gi|355482652|gb|AES63855.1| Dof zinc finger protein-like protein [Medicago truncatula]

 Score =  131 bits (329), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 54/66 (81%), Positives = 59/66 (89%)

Query: 26 GTENQQQQEQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVG 85
          G  ++  Q  PQPQKCPRC+S NTKFCYYNNYSLSQPR+FCKTCRRYWTQGGTLRNVP+G
Sbjct: 12 GEMSKLVQAHPQPQKCPRCDSFNTKFCYYNNYSLSQPRFFCKTCRRYWTQGGTLRNVPIG 71

Query: 86 GGCRKG 91
          GGCRKG
Sbjct: 72 GGCRKG 77

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	336
TAIR|locus:2170753	372	HCA2 "HIGH CAMBIAL ACTIVITY2"	0.133	0.120	0.911	2.5e-26
TAIR|locus:2032153	325	AT1G28310 [Arabidopsis thalian	0.133	0.138	0.866	1.2e-24
TAIR|locus:2039959	369	DAG2 "DOF AFFECTING GERMINATIO	0.178	0.162	0.683	4.5e-24
TAIR|locus:2053175	340	AT2G28810 [Arabidopsis thalian	0.133	0.132	0.8	5.4e-23
TAIR|locus:2134981	342	AT4G24060 [Arabidopsis thalian	0.130	0.128	0.840	2.9e-22
TAIR|locus:2056588	288	AT2G28510 [Arabidopsis thalian	0.130	0.152	0.931	4.9e-21
TAIR|locus:2133064	232	DOF4.3 "AT4G21040" [Arabidopsi	0.130	0.189	0.795	5.2e-21
TAIR|locus:2144030	257	TMO6 "TARGET OF MONOPTEROS 6"	0.133	0.175	0.844	1e-20
TAIR|locus:2094746	204	DOF2 "DOF zinc finger protein	0.193	0.318	0.646	1.3e-20
TAIR|locus:2040746	330	DOF2.4 "DNA binding with one f	0.133	0.136	0.866	2.1e-20

TAIR|locus:2170753 HCA2 "HIGH CAMBIAL ACTIVITY2" [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 2.5e-26, Sum P(2) = 2.5e-26
 Identities = 41/45 (91%), Positives = 44/45 (97%)

Query:    40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             KCPRCES +TKFCYYNNYSLSQPRYFCKTCRRYWT+GGTLRN+PV
Sbjct:    74 KCPRCESTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPV 118

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;TAS

GO:0010067 "procambium histogenesis" evidence=IMP

GO:0010087 "phloem or xylem histogenesis" evidence=IMP

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

TAIR|locus:2032153 AT1G28310 [Arabidopsis thaliana (taxid:3702)]

 Score = 241 (89.9 bits), Expect = 1.2e-24, Sum P(2) = 1.2e-24
 Identities = 39/45 (86%), Positives = 43/45 (95%)

Query:    40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             KCPRC+S NTKFCYYNNYSLSQPR+FCK C+RYWT+GGTLRNVPV
Sbjct:    42 KCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPV 86

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 238 (88.8 bits), Expect = 4.5e-24, Sum P(2) = 4.5e-24
 Identities = 41/60 (68%), Positives = 44/60 (73%)

Query:    41 CPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVXXXXXXXXXXXXSSVS 100
             CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWT+GG+LRNVPV            SS S
Sbjct:    82 CPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGSSRKNKRSSSSSSS 141

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

 Score = 230 (86.0 bits), Expect = 5.4e-23, Sum P(2) = 5.4e-23
 Identities = 36/45 (80%), Positives = 42/45 (93%)

Query:    40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             KCPRC+S NTKFCY+NNY+L+QPR+FCK CRRYWT+GG LRNVPV
Sbjct:    95 KCPRCDSANTKFCYFNNYNLTQPRHFCKACRRYWTRGGALRNVPV 139

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:2134981 AT4G24060 [Arabidopsis thaliana (taxid:3702)]

 Score = 234 (87.4 bits), Expect = 2.9e-22, Sum P(2) = 2.9e-22
 Identities = 37/44 (84%), Positives = 41/44 (93%)

Query:    41 CPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWT+GG+LRN+PV
Sbjct:    55 CPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNIPV 98

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:2056588 AT2G28510 [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 41/44 (93%), Positives = 43/44 (97%)

Query:    41 CPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             CPRCES NTKFCYYNNYSLSQPRYFCK+CRRYWT+GGTLRNVPV
Sbjct:    50 CPRCESPNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPV 93

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:0005730 "nucleolus" evidence=IDA

TAIR|locus:2133064 DOF4.3 "AT4G21040" [Arabidopsis thaliana (taxid:3702)]

 Score = 214 (80.4 bits), Expect = 5.2e-21, Sum P(2) = 5.2e-21
 Identities = 35/44 (79%), Positives = 37/44 (84%)

Query:    41 CPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             C RC+S NTKFCYYNNYS  QPRYFCK CRRYWT GG LRNVP+
Sbjct:    27 CARCDSDNTKFCYYNNYSEFQPRYFCKNCRRYWTHGGALRNVPI 70

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0043565 "sequence-specific DNA binding" evidence=IDA

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

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

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 38/45 (84%), Positives = 44/45 (97%)

Query:    40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             +CPRC+S NTKFCYYNNYSL+QPRYFCK+CRRYWT+GGTLRN+PV
Sbjct:    56 RCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPV 100

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

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 42/65 (64%), Positives = 48/65 (73%)

Query:    40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVXXXXXXXXXXXXSSV 99
             KCPRC+S NTKFCYYNNY+LSQPR+FCK+CRRYWT+GG LRNVPV            +S 
Sbjct:    30 KCPRCDSPNTKFCYYNNYNLSQPRHFCKSCRRYWTKGGALRNVPVGGGSRKNATKRSTSS 89

Query:   100 SGEAS 104
             S  AS
Sbjct:    90 SSSAS 94

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

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 39/45 (86%), Positives = 43/45 (95%)

Query:    40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV 84
             KCPRCES NTKFCY+NNYSL+QPR+FCKTCRRYWT+GG LRNVPV
Sbjct:    90 KCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPV 134

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0010089 "xylem development" evidence=RCA

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

---

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: GSVIVG00003074001 SubName- Full=Chromosome chr10 scaffold_138, whole genome shotgun sequence; (299 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	336
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	5e-37

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

 Score =  126 bits (319), Expect = 5e-37
 Identities = 45/63 (71%), Positives = 53/63 (84%)

Query: 34 EQPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKR 93
          +  +  KCPRC+S+NTKFCYYNNY+L+QPRYFCK CRRYWT GG LRNVPVGGG RK KR
Sbjct: 1  KPDKALKCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKR 60

Query: 94 TKT 96
          + +
Sbjct: 61 SSS 63

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	336
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	92.77
COG3677	129	Transposase and inactivated derivatives [DNA repli	91.91
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	90.62
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	90.2
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	87.8
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	84.5
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	81.95
cd00202	54	ZnF_GATA Zinc finger DNA binding domain; binds spe	80.72

>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=7.8e-37  Score=233.66  Aligned_cols=62  Identities=79%  Similarity=1.600  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccCCCCccCCCCCCC
Q 042156           35 QPQPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPVGGGCRKGKRTKT   96 (336)
Q Consensus        35 ~~~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPVGGG~RKnKrs~s   96 (336)
                      ++++++||||+|++|||||||||+++||||||++|+||||+||+||||||||||||+|++++
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            57899999999999999999999999999999999999999999999999999999998753

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=92.77  E-value=0.043  Score=47.70  Aligned_cols=34  Identities=26%  Similarity=0.773  Sum_probs=27.1

Q ss_pred             CCCCCCCCCCCceeeeeccc--CCCCCccccccccccc
Q 042156           38 PQKCPRCESLNTKFCYYNNY--SLSQPRYFCKTCRRYW   73 (336)
Q Consensus        38 ~~~CPRC~S~nTKFcYyNNy--~~~QPRhfCksCrRYW   73 (336)
                      ...||||.|.+|+..  +.|  +.+..-|+|++|+.=+
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            579999999999974  555  4557779999998644

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

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

Probab=91.91  E-value=0.12  Score=44.12  Aligned_cols=37  Identities=32%  Similarity=0.666  Sum_probs=29.0

Q ss_pred             CCCCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 042156           37 QPQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQ   75 (336)
Q Consensus        37 ~~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~   75 (336)
                      ....||+|.+.+  +-=+.-+.....||.|++|++-|+.
T Consensus        29 ~~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~   65 (129)
T COG3677          29 TKVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV   65 (129)
T ss_pred             ccCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence            458899999999  2235555555999999999998874

>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=90.62  E-value=0.25  Score=34.98  Aligned_cols=28  Identities=39%  Similarity=0.844  Sum_probs=22.4

Q ss_pred             CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 042156           38 PQKCPRCESLNTKFCYYNNYSLSQPRYFCKTCRR   71 (336)
Q Consensus        38 ~~~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrR   71 (336)
                      ...||+|.+.  +...+.+    ..++.|++|++
T Consensus        18 g~~CP~Cg~~--~~~~~~~----~~~~~C~~C~~   45 (46)
T PF12760_consen   18 GFVCPHCGST--KHYRLKT----RGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCCCe--eeEEeCC----CCeEECCCCCC
Confidence            4669999998  6655555    78899999985

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

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

Probab=90.20  E-value=0.2  Score=35.06  Aligned_cols=31  Identities=42%  Similarity=0.793  Sum_probs=21.5

Q ss_pred             CCCCCCCCCCCceeeeecccCC-CCCcccccccc
Q 042156           38 PQKCPRCESLNTKFCYYNNYSL-SQPRYFCKTCR   70 (336)
Q Consensus        38 ~~~CPRC~S~nTKFcYyNNy~~-~QPRhfCksCr   70 (336)
                      .+.||+|.+.+.-  |=|-.+. -..||+|++|+
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            5789999998721  1233333 35899999996

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

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=87.80  E-value=0.59  Score=32.80  Aligned_cols=37  Identities=27%  Similarity=0.793  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 042156           39 QKCPRCESLNTKFCYYNNYSLSQP---RYFCKTCRRYWTQ   75 (336)
Q Consensus        39 ~~CPRC~S~nTKFcYyNNy~~~QP---RhfCksCrRYWT~   75 (336)
                      .+||+|...+.-|-..+-.+...|   -|.|.+|...|..
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            379999988777766665655555   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=84.50  E-value=0.84  Score=31.79  Aligned_cols=36  Identities=31%  Similarity=0.769  Sum_probs=24.5

Q ss_pred             CCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 042156           39 QKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWT   74 (336)
Q Consensus        39 ~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT   74 (336)
                      .+||.|...+.-|--.+.....-|-   |.|.+|..-|+
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr   39 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR   39 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence            3799999988776555555555553   89999999985

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=81.95  E-value=0.68  Score=43.00  Aligned_cols=37  Identities=24%  Similarity=0.554  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCCC-ceeeeecc-cCCCCCccccccccccc
Q 042156           37 QPQKCPRCESLN-TKFCYYNN-YSLSQPRYFCKTCRRYW   73 (336)
Q Consensus        37 ~~~~CPRC~S~n-TKFcYyNN-y~~~QPRhfCksCrRYW   73 (336)
                      ....||.|...+ .++-||.. -....--+.|+.|+.|+
T Consensus       210 ~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl  248 (290)
T PF04216_consen  210 VRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL  248 (290)
T ss_dssp             -TTS-TTT---SS-EEE--------SEEEEEETTTTEEE
T ss_pred             cCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH
Confidence            577899999855 56667633 33333348999999997

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.

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

Probab=80.72  E-value=1.3  Score=32.88  Aligned_cols=42  Identities=24%  Similarity=0.613  Sum_probs=29.7

Q ss_pred             CCCCCCCCCceeeeecccCCCCCcccccccccccccCcccccccC
Q 042156           40 KCPRCESLNTKFCYYNNYSLSQPRYFCKTCRRYWTQGGTLRNVPV   84 (336)
Q Consensus        40 ~CPRC~S~nTKFcYyNNy~~~QPRhfCksCrRYWT~GGtLRNVPV   84 (336)
                      .|-.|...+|..=.-.   ......+|-+|..||.+.|..|-+-.
T Consensus         1 ~C~~C~~~~Tp~WR~g---~~~~~~LCNaCgl~~~k~~~~rp~~~   42 (54)
T cd00202           1 ACSNCGTTTTPLWRRG---PSGGSTLCNACGLYWKKHGVMRPLSK   42 (54)
T ss_pred             CCCCCCCCCCcccccC---CCCcchHHHHHHHHHHhcCCCCCccc
Confidence            3777888777532222   24677999999999999997655444

---

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

No hit with probability above 80.00

---

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	336
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	90.83
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	87.5

>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=90.83  E-value=0.15  Score=37.48  Aligned_cols=45  Identities=18%  Similarity=0.472  Sum_probs=33.9

Q ss_pred             CCCCCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccCcc
Q 042156           34 EQPQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYWTQGGT   78 (336)
Q Consensus        34 ~~~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYWT~GGt   78 (336)
                      .+..-..||+|...+.-|-+.+-.+..-|-   |.|..|.-.|+.-.+
T Consensus        19 lp~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~~~~   66 (72)
T d1twfi2          19 LPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQK   66 (72)
T ss_dssp             SCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECCTT
T ss_pred             CCccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCcccccc
Confidence            345568999999888877666665544444   899999999998544

>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=87.50  E-value=0.2  Score=34.68  Aligned_cols=38  Identities=21%  Similarity=0.593  Sum_probs=31.8

Q ss_pred             CCCCCCCCCCCCCceeeeecccCCCCCc---cccccccccc
Q 042156           36 PQPQKCPRCESLNTKFCYYNNYSLSQPR---YFCKTCRRYW   73 (336)
Q Consensus        36 ~~~~~CPRC~S~nTKFcYyNNy~~~QPR---hfCksCrRYW   73 (336)
                      ...++||+|.+.+..|--++..+...|-   +.|..|..-|
T Consensus         7 T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~W   47 (50)
T d1tfia_           7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRW   47 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEE
T ss_pred             cCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCee
Confidence            4578999999999887777777777776   8999999888