Citrus Sinensis ID: 025998

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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-----
Protein Sequence
MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDNWTSFDLPGFELYSRP
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEccccccccHHHHHcccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEEcccccccccHHHHHHHHHEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccc
Coil and Loop (DISEMBL)
mekkwkpdvetapscprcaspntkfcyynnyslsqpryfckgcrrywtkggslrnvpvgggcrkngrakssrrkspfnndrpkascssdhtddavstpnggsdIDLAVVFAnsstpdnvvqnddfnvhnvmgngdlnilgefpqvfgqlqEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWsdqaetetlpnftWQRAMFQlqdfdsfpaddqLKASANlisdnwtsfdlpgfelysrp
Flexible Loop (DISEMBL)
mekkwkpdvetapscprcaspntKFCYYNNYSLSQPRYFCKGCRRYWTKggslrnvpvgggcrkngrakssrrkspfnndrpkascssdhtddAVSTPNGGSDIDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASAnlisdnwtsfdlpgfelysrp
Low Complexity Region (SEG)
MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDNWTSFDLPGFELYSRP
Disordered region (IsUnstruct)
******************ASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVG********************************************IDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDNWTSFDLPGFEL****
Disordered Region (DISOPRED)
*****************CASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLR**************************************************************************************************************************************************************************NLISDNWTSFDLPGFELYS**
Disordered Region (DISEMBL)
**************CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGC***********************************PNGGSDIDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDNWTSFDLPGFELYSRP
Disordered Region (DISPRO)
*****KPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVG********************************************IDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFG******D**V*DFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQ***SFP*****KASANLI******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDNWTSFDLPGFELYSRP
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	245	2.2.26 [Sep-21-2011]
P68349	260	Dof zinc finger protein D	yes	no	0.718	0.676	0.443	5e-36
Q9SVC5	247	Dof zinc finger protein D	no	no	0.412	0.408	0.606	3e-31
Q84TE9	257	Dof zinc finger protein D	no	no	0.567	0.540	0.448	1e-27
Q8LE43	288	Dof zinc finger protein D	no	no	0.244	0.208	0.85	2e-26
Q8LAP8	342	Dof zinc finger protein D	no	no	0.269	0.192	0.757	2e-26
Q43385	296	Dof zinc finger protein D	no	no	0.685	0.567	0.361	3e-26
O24463	328	Dof zinc finger protein P	N/A	no	0.273	0.204	0.731	5e-26
Q8LDR0	307	Dof zinc finger protein D	no	no	0.322	0.257	0.632	3e-25
Q9LSL6	316	Dof zinc finger protein D	no	no	0.220	0.170	0.814	4e-24
O80928	330	Dof zinc finger protein D	no	no	0.244	0.181	0.766	4e-24

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

 Score =  151 bits (381), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 91/205 (44%), Positives = 118/205 (57%), Gaps = 29/205 (14%)

Query: 1   MEKKWKPDVE----TAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNV 56
           + +KWK   E    TAP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRN+
Sbjct: 22  IPEKWKLSYEQEAITAPACPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNI 81

Query: 57  PVGGGCRKNGRAK-SSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFA---- 111
           PVGGGCRK  R++ +S ++   N +RP       + DD   +   GSDIDLA VFA    
Sbjct: 82  PVGGGCRKRSRSRQNSHKRFGRNENRPDGLI---NQDDGFQSSPPGSDIDLAAVFAQYVT 138

Query: 112 --NSSTPDNVVQNDD-----FNVHNVMG---------NGDLNILGEFPQVFGQLQEEEDR 155
             + S+ DN   +D         H +           + DL   GEF  +  + +E+++ 
Sbjct: 139 DRSPSSTDNTTGSDQDSPITTTTHALESLSWDICQETDVDLGFYGEFNNLTQKTKEDQEV 198

Query: 156 RVQDFLEDDMVNAHGLQALLGDEIV 180
             Q FL++D       Q LL D+ +
Sbjct: 199 FGQ-FLQEDREEIFEFQGLLDDKEI 222

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 =  135 bits (340), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 71/117 (60%), Positives = 80/117 (68%), Gaps = 16/117 (13%)

Query: 5   WKPDV----ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
           W+P+     E  PSCPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWTKGGSLRNVPVGG
Sbjct: 13  WRPNANANAEITPSCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVGG 72

Query: 61  GCRKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGS-DIDLAVVFANSSTP 116
           GCRK+ R KSS      NN +   + +S         P GGS  IDLA+V+AN   P
Sbjct: 73  GCRKSRRPKSSSG----NNTKTSLTANS-------GNPGGGSPSIDLALVYANFLNP 118

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  123 bits (309), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 66/147 (44%), Positives = 87/147 (59%), Gaps = 8/147 (5%)

Query: 10  ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAK 69
           E A  CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWTKGG+LRN+PVGGGCRKN R+ 
Sbjct: 52  ELALRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPVGGGCRKNKRST 111

Query: 70  SSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFA--NSSTPDNVVQNDDFNV 127
           SS  +S      P +      +    +  +    IDL++ FA  N   P +  Q      
Sbjct: 112 SSAARSLRTTPEPASHDGKVFSAAGFNGYSNNEHIDLSLAFALLNKQHPGSSSQ---LGF 168

Query: 128 HNVMGNGDLNILGEFPQVFGQLQEEED 154
           H+ +G+   +   +   +FG  Q++E+
Sbjct: 169 HSELGSSHQS---DMEGMFGTSQQKEN 192

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 =  119 bits (298), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 55/60 (91%)

Query: 12  APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSS 71
           A +CPRC SPNTKFCYYNNYSLSQPRYFCK CRRYWTKGG+LRNVPVGGGCR+N R+ SS
Sbjct: 47  AQNCPRCESPNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPVGGGCRRNKRSSSS 106

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

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 =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 58/66 (87%)

Query: 2   EKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGG 61
           E+K +P+ + A +CPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWT+GGSLRN+PVGGG
Sbjct: 42  ERKARPEKDQAVNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNIPVGGG 101

Query: 62  CRKNGR 67
            RKN R
Sbjct: 102 SRKNKR 107

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 =  119 bits (297), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 78/216 (36%), Positives = 106/216 (49%), Gaps = 48/216 (22%)

Query: 15  CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSSRRK 74
           CPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWT+GGSLRNVPVGG  RKN R+ S+   
Sbjct: 76  CPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGSSRKNKRS-STPLA 134

Query: 75  SPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSSTPDNVVQNDDFNVHNVMGNG 134
           SP N   P                    D++  ++F+ S  P+               N 
Sbjct: 135 SPSNPKLP--------------------DLNPPILFS-SQIPNK-------------SNK 160

Query: 135 DLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETE 194
           DLN+L  FP     + ++      + L  + V++ G+   L  +++D    L+S      
Sbjct: 161 DLNLL-SFP-----VMQDHHHHALELLRSNGVSSRGMNTFLPGQMMDSNSVLYSSLG-FP 213

Query: 195 TLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDN 230
           T+P++       Q  +  SF  D       N I+ N
Sbjct: 214 TMPDYK------QSNNNLSFSIDHHQGIGHNTINSN 243

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

 Score =  118 bits (295), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 49/67 (73%), Positives = 55/67 (82%)

Query: 2   EKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGG 61
           E+K +P +  A  CPRC S NTKFCYYNNYS+SQPRYFCK CRRYWT GG+LRNVP+GGG
Sbjct: 49  ERKPRPQLPEALKCPRCDSNNTKFCYYNNYSMSQPRYFCKACRRYWTHGGTLRNVPIGGG 108

Query: 62  CRKNGRA 68
           CRKN  A
Sbjct: 109 CRKNKHA 115

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

Zea mays (taxid: 4577)

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

 Score =  115 bits (288), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 50/79 (63%), Positives = 60/79 (75%)

Query: 15  CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSSRRK 74
           CPRC S NTKFCYYNNY+LSQPR+FCK CRRYWTKGG LRNVPVGGGCRK  R+K+ +  
Sbjct: 53  CPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKAKRSKTKQVP 112

Query: 75  SPFNNDRPKASCSSDHTDD 93
           S  + D+P  +    H ++
Sbjct: 113 SSSSADKPTTTQDDHHVEE 131

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  111 bits (278), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 44/54 (81%), Positives = 50/54 (92%)

Query: 15 CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRA 68
          CPRC SPNTKFCYYNNYSLSQPR+FCK CRRYWT+GG+LRNVP+GGGCRK  ++
Sbjct: 43 CPRCNSPNTKFCYYNNYSLSQPRHFCKSCRRYWTRGGALRNVPIGGGCRKTKKS 96

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 =  111 bits (278), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 52/60 (86%)

Query: 10  ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAK 69
           E A  CPRC S NTKFCY+NNYSL+QPR+FCK CRRYWT+GG+LRNVPVGGGCR+N R K
Sbjct: 86  EAALKCPRCESTNTKFCYFNNYSLTQPRHFCKTCRRYWTRGGALRNVPVGGGCRRNRRTK 145

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

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	245
224085085	293	f-box family protein [Populus trichocarp	0.963	0.805	0.506	1e-62
224062922	301	f-box family protein [Populus trichocarp	0.971	0.790	0.513	7e-61
255570374	294	hypothetical protein RCOM_0137680 [Ricin	0.979	0.816	0.506	2e-57
225457735	281	PREDICTED: dof zinc finger protein DOF3.	0.930	0.811	0.458	2e-51
356507602	289	PREDICTED: dof zinc finger protein DOF3.	0.955	0.809	0.420	4e-37
357463751	332	Dof zinc finger protein [Medicago trunca	0.914	0.674	0.394	2e-36
356518609	289	PREDICTED: dof zinc finger protein DOF3.	0.930	0.788	0.396	3e-36
15218970	260	Dof zinc finger protein DOF1.2 [Arabidop	0.718	0.676	0.443	3e-34
116830897	261	unknown [Arabidopsis thaliana]	0.718	0.674	0.443	3e-34
356537198	288	PREDICTED: dof zinc finger protein DOF3.	0.946	0.805	0.368	6e-34

>gi|224085085|ref|XP_002307484.1| f-box family protein [Populus trichocarpa] gi|222856933|gb|EEE94480.1| f-box family protein [Populus trichocarpa]

 Score =  245 bits (626), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 147/290 (50%), Positives = 171/290 (58%), Gaps = 54/290 (18%)

Query: 2   EKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGG 61
           EKKWK  VE AP+CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGS+RNVPVGGG
Sbjct: 12  EKKWKSKVEAAPNCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSIRNVPVGGG 71

Query: 62  CRKNGRAKSSRRKSPFNNDRPKAS------------CSSDHTDDAVSTPNGGSDIDLAVV 109
           CRK  RAKSS+      N+R   S            CS++    A      GSDIDLAVV
Sbjct: 72  CRKYRRAKSSKVS---QNERAAVSVNYSRTNETTLACSTNKDSMAQQGGANGSDIDLAVV 128

Query: 110 FA------------------------------NSSTPDNVVQNDDF--NVHNVMGNGDLN 137
           FA                              NSS P +  QND    ++       + N
Sbjct: 129 FAKFLNQDLSYEPDFTGEELLNEGGDQMVDVSNSSNPSDSFQNDSMMESLKRSDQIQESN 188

Query: 138 IL-GEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETL 196
           +L G+   + G+ Q  E+ R+Q+ +E   +NA GLQ LL DEIV  Q ALWSD A     
Sbjct: 189 LLEGQSQVLVGEKQRLEEERIQELIESQDMNAFGLQDLLSDEIV--QDALWSDDATLTNF 246

Query: 197 PNFTWQRAMFQLQDFDSFPADDQLKASANLISDN-WTSFDLPGFELYSRP 245
           PN  WQ  M QLQDFDSF  DD+LK S+N ISDN W+S DL GFE++SRP
Sbjct: 247 PN--WQ-PMLQLQDFDSFSVDDRLKISSNFISDNSWSSLDLSGFEVFSRP 293

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224062922|ref|XP_002300933.1| f-box family protein [Populus trichocarpa] gi|222842659|gb|EEE80206.1| f-box family protein [Populus trichocarpa]

 Score =  239 bits (610), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 149/290 (51%), Positives = 177/290 (61%), Gaps = 52/290 (17%)

Query: 1   MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
           ME+KWK ++E AP+CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVP GG
Sbjct: 19  MERKWKSNIEVAPNCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPAGG 78

Query: 61  GCRKNGRAKSSR----RKSPFNNDRPKA----SCSSDHTDDAVSTPNGGSDIDLAVVF-- 110
           GCRK  RA+SS+     ++  + D  +A    +CSS+    A      GSDIDLA VF  
Sbjct: 79  GCRKYRRARSSKISQNERAAVSLDYSRANETLACSSNKDSVAQQDGANGSDIDLAAVFSK 138

Query: 111 ---------------------------ANSSTP-DNVVQNDDFNVHNVMGNGDL----NI 138
                                      +NSSTP  +  QND   +   +   DL    N+
Sbjct: 139 FLNQDLSYGPEFIGEELRDEGSELVNISNSSTPISDSYQNDP--MMESLKRSDLTQESNL 196

Query: 139 LGEFPQVF-GQLQE-EEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETL 196
           L    QV  G+ Q+ EED+R Q+ +E   +NA GLQ LL DEIV  Q ALWSD A    +
Sbjct: 197 LEGRSQVLVGEKQQFEEDQRFQELIESQDMNAFGLQNLLIDEIV--QDALWSDDATLPHV 254

Query: 197 PNFTWQRAMFQLQDFDSFPADDQLKASANLIS-DNWTSFDLPGFELYSRP 245
           PN  WQ  M QLQDFDSF  DD+LK SAN  S DNW+SFDL GFE++ RP
Sbjct: 255 PN--WQ-PMVQLQDFDSFSVDDRLKISANFTSDDNWSSFDLSGFEVFPRP 301

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570374|ref|XP_002526146.1| hypothetical protein RCOM_0137680 [Ricinus communis] gi|223534523|gb|EEF36222.1| hypothetical protein RCOM_0137680 [Ricinus communis]

 Score =  228 bits (581), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 145/286 (50%), Positives = 168/286 (58%), Gaps = 46/286 (16%)

Query: 1   MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
           ME KWK  VE APSCPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG
Sbjct: 11  MEGKWKTHVELAPSCPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 70

Query: 61  GCRKNGRAKSSRRKSP------FNNDRPKASCSS--DHTDDAVSTPNGGSDIDLAVVFAN 112
           GCRK+ RAKSSR          FN     +SCSS  D T     + N GS+IDLAVVFA 
Sbjct: 71  GCRKSRRAKSSRGAVSMNYGKNFNGPLSGSSCSSNMDSTVQETGSNNDGSEIDLAVVFAK 130

Query: 113 --------------SSTPDNVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQ 158
                            PD     +  +V N +   D + + E   + G+  +E +  +Q
Sbjct: 131 FLNQESSFQPEFVGKELPDEPSDQELVSVANSLSPPDSDAVIECQNLIGESIQESNDLLQ 190

Query: 159 DFL----------------EDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQ 202
             L                E   +N  GLQ LLGDEIV  Q ALWS+ AET +L N TWQ
Sbjct: 191 ALLVAGNQDQEQGDQEMIMESQDMNEFGLQTLLGDEIV--QDALWSE-AET-SLSNVTWQ 246

Query: 203 RAMFQL--QDFDSFPADDQLKASANLISDN-WTSFDL-PGFELYSR 244
             + Q+  Q FDSF  DDQLK   NLI+DN W+SFDL  GFE++SR
Sbjct: 247 IPVDQVQPQGFDSFSVDDQLKIPTNLINDNAWSSFDLSAGFEVFSR 292

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457735|ref|XP_002262622.1| PREDICTED: dof zinc finger protein DOF3.5-like [Vitis vinifera]

 Score =  207 bits (528), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 123/268 (45%), Positives = 152/268 (56%), Gaps = 40/268 (14%)

Query: 1   MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
           ++K WK + E APSCPRC+SPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG
Sbjct: 20  LDKGWKSNAELAPSCPRCSSPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 79

Query: 61  GCRKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVSTP---NGGSDIDLAVVFAN----- 112
           GCRKN R K+ R            S +    D  V  P    GG++IDLAVVFA      
Sbjct: 80  GCRKNRRGKAVRVPQLERGSGNYGSDAPPSGDSVVVVPPGRTGGAEIDLAVVFAKFLNHN 139

Query: 113 ----SSTPDNVVQNDDFNVHNVMG--NGD-------------LNILGEFPQVFGQLQ--- 150
                    + + +      NV+G  N D             L+++GE   + G  Q   
Sbjct: 140 SGFEPEVAGSALSDQTDAAGNVLGALNSDAQQEDMAMECGTSLDLMGEVQLLEGHTQLFD 199

Query: 151 ----EEEDRRVQDFLEDDMVNAHGLQALLGDEIVDHQVALWSDQAETETLPNFTWQRAMF 206
               + ++ R+Q+F   D  +A+GL  LL DE    Q  LWSD    +TL NFTWQ  M 
Sbjct: 200 GGEKQIQEERIQEFTSHDDASAYGLPTLLSDEAA--QEVLWSD---AQTLQNFTWQPVM- 253

Query: 207 QLQDFDSFPADDQLKASANLISDNWTSF 234
           QLQ+F+S P+ D  K S NLI + W+SF
Sbjct: 254 QLQEFESVPSYDHSKMSPNLIGEFWSSF 281

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507602|ref|XP_003522553.1| PREDICTED: dof zinc finger protein DOF3.5 [Glycine max]

 Score =  160 bits (405), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 108/257 (42%), Positives = 139/257 (54%), Gaps = 23/257 (8%)

Query: 4   KWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 63
           +WKP VE AP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR
Sbjct: 35  RWKPSVEVAPNCPRCASTNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 94

Query: 64  KNGRAKSSRRKSPFNNDRPKA-SC----SSDHTDDAVSTPNGGSDIDLAVVFANSSTPDN 118
           KN R KSS      +    +A SC    SS   DDA    N   DID+A+VFA    P  
Sbjct: 95  KNRRGKSSSSSRLQHQSHQRAFSCENTESSSVGDDAQQNNNVSRDIDMALVFAKFLNPKP 154

Query: 119 VVQNDDF---NVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALL 175
               D+    + +N +    + I  +   V  Q +   D  + +     +V    L+ LL
Sbjct: 155 TTGEDNNGSPSSNNYLTPESVEIEND-AVVQSQNKASSDPVIVESENLSLVEIDELERLL 213

Query: 176 GDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADD-----QLKASANLISD- 229
           G  +   +  LWSD   + ++   TW+  + + +       DD      +  SA+ +SD 
Sbjct: 214 G--VCGDEDGLWSDATLSSSV---TWEPPLKESEYSMPLNEDDGDQLLPIIISASTMSDT 268

Query: 230 ---NWTSFDLPGFELYS 243
              NW+SFDL   +  S
Sbjct: 269 CWSNWSSFDLSTMDALS 285

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463751|ref|XP_003602157.1| Dof zinc finger protein [Medicago truncatula] gi|355491205|gb|AES72408.1| Dof zinc finger protein [Medicago truncatula]

 Score =  158 bits (400), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 119/302 (39%), Positives = 147/302 (48%), Gaps = 78/302 (25%)

Query: 4   KWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 63
           KWKP +E AP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR
Sbjct: 42  KWKPHIEIAPNCPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 101

Query: 64  KNGRAKSSRRKSPFNNDRPKASC-SSDHTDDAVSTPNGGSDIDLAVVFANSSTPDNVVQN 122
           KN R K+ R       DR  A+  S+D  D   +  NG  DID+AVVFA       + QN
Sbjct: 102 KNRRGKAVRNSQ---TDRLSANYGSADDEDHQQNQNNGSRDIDMAVVFAKF-----LNQN 153

Query: 123 DDFNVHNVMGNGDLNILGEFPQVFG---------------QLQEEEDRRVQDFLEDDMVN 167
            +   H   G+ +L I  E                      ++ E D  VQ     D V 
Sbjct: 154 PNSTHH---GDEELEIESEVNNNGLSSSSNNINNLSSTPESVETENDAVVQPHKPFDEVQ 210

Query: 168 AHG--------------LQALLG-DEIVDHQVALWSD-----QAETETLPNFTWQR--AM 205
            +G               +  LG DE V   V LW D        + +  N+TWQ+   M
Sbjct: 211 NYGGEHELSLSGIEYDQFEGFLGVDEDVVQDV-LWPDSNAMNMMMSSSSNNYTWQQPPPM 269

Query: 206 FQLQDFDSFPADDQLK---------------------ASANLISDNWT---SFDLPGFEL 241
            Q++     P + +L+                      S NLIS++W    SFDL   E+
Sbjct: 270 MQME----LPGELELEYSMPLPLPLNNENGTINSNSTTSVNLISESWNSWDSFDLSTMEV 325

Query: 242 YS 243
           +S
Sbjct: 326 FS 327

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518609|ref|XP_003527971.1| PREDICTED: dof zinc finger protein DOF3.5-like [Glycine max]

 Score =  157 bits (398), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 104/262 (39%), Positives = 133/262 (50%), Gaps = 34/262 (12%)

Query: 4   KWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 63
           +WKP VE AP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR
Sbjct: 36  RWKPSVEVAPNCPRCASTNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCR 95

Query: 64  KNGRAKSSRRKSPFNNDRPKASCSSDHT--DDAVSTPNGGSDIDLAVVFANSSTPDNVVQ 121
           KN R KS +  S               +   DA    NG  DID+A+VFA    P     
Sbjct: 96  KNRRGKSLQSSSSRQQRASSFVSGDTESSFSDAQQINNGSRDIDMALVFAKFLNPKPTTG 155

Query: 122 ND---------DFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQ 172
            D         +F   +V    D         V  Q +   D  + +     +     L+
Sbjct: 156 EDNNGSSSTSNNFTPESVEIENDA-------VVQSQNKASSDPVIVESENLSLGEIDELE 208

Query: 173 ALLGDEIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQ-------LKASAN 225
            LLG  +   +  LWSD   + ++   TW+  + +L+       DD        + +++ 
Sbjct: 209 RLLG--VCGDEDGLWSDATLSSSV---TWEPPLKELEYSMPLNEDDDDAQLLPIITSAST 263

Query: 226 LISD----NWTSFDLPGFELYS 243
           +ISD    NW+SFDL   E +S
Sbjct: 264 MISDSCWSNWSSFDLSTMEAFS 285

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218970|ref|NP_173556.1| Dof zinc finger protein DOF1.2 [Arabidopsis thaliana] gi|55583798|sp|P68349.1|DOF12_ARATH RecName: Full=Dof zinc finger protein DOF1.2; Short=AtDOF1.2 gi|91805817|gb|ABE65637.1| Dof-type zinc finger domain-containing protein [Arabidopsis thaliana] gi|225897956|dbj|BAH30310.1| hypothetical protein [Arabidopsis thaliana] gi|332191968|gb|AEE30089.1| Dof zinc finger protein DOF1.2 [Arabidopsis thaliana]

 Score =  151 bits (381), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 91/205 (44%), Positives = 118/205 (57%), Gaps = 29/205 (14%)

Query: 1   MEKKWKPDVE----TAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNV 56
           + +KWK   E    TAP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRN+
Sbjct: 22  IPEKWKLSYEQEAITAPACPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNI 81

Query: 57  PVGGGCRKNGRAK-SSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFA---- 111
           PVGGGCRK  R++ +S ++   N +RP       + DD   +   GSDIDLA VFA    
Sbjct: 82  PVGGGCRKRSRSRQNSHKRFGRNENRPDGLI---NQDDGFQSSPPGSDIDLAAVFAQYVT 138

Query: 112 --NSSTPDNVVQNDD-----FNVHNVMG---------NGDLNILGEFPQVFGQLQEEEDR 155
             + S+ DN   +D         H +           + DL   GEF  +  + +E+++ 
Sbjct: 139 DRSPSSTDNTTGSDQDSPITTTTHALESLSWDICQETDVDLGFYGEFNNLTQKTKEDQEV 198

Query: 156 RVQDFLEDDMVNAHGLQALLGDEIV 180
             Q FL++D       Q LL D+ +
Sbjct: 199 FGQ-FLQEDREEIFEFQGLLDDKEI 222

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116830897|gb|ABK28405.1| unknown [Arabidopsis thaliana]

 Score =  151 bits (381), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 91/205 (44%), Positives = 118/205 (57%), Gaps = 29/205 (14%)

Query: 1   MEKKWKPDVE----TAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNV 56
           + +KWK   E    TAP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRN+
Sbjct: 22  IPEKWKLSYEQEAITAPACPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNI 81

Query: 57  PVGGGCRKNGRAK-SSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFA---- 111
           PVGGGCRK  R++ +S ++   N +RP       + DD   +   GSDIDLA VFA    
Sbjct: 82  PVGGGCRKRSRSRQNSHKRFGRNENRPDGLI---NQDDGFQSSPPGSDIDLAAVFAQYVT 138

Query: 112 --NSSTPDNVVQNDD-----FNVHNVMG---------NGDLNILGEFPQVFGQLQEEEDR 155
             + S+ DN   +D         H +           + DL   GEF  +  + +E+++ 
Sbjct: 139 DRSPSSTDNTTGSDQDSPITTTTHALESLSWDICQETDVDLGFYGEFNNLTQKTKEDQEV 198

Query: 156 RVQDFLEDDMVNAHGLQALLGDEIV 180
             Q FL++D       Q LL D+ +
Sbjct: 199 FGQ-FLQEDREEIFEFQGLLDDKEI 222

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537198|ref|XP_003537116.1| PREDICTED: dof zinc finger protein DOF3.5-like [Glycine max]

 Score =  150 bits (378), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 111/301 (36%), Positives = 145/301 (48%), Gaps = 69/301 (22%)

Query: 1   MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
           ME  WKP+VE +P+CPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWTKGGSLRNVPVGG
Sbjct: 1   MESGWKPEVEISPNCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVGG 60

Query: 61  GCRKNGRAKSSRRKSPFNNDRPKAS-----CSSDHTDDAVSTPNGGSDIDLAVVFAN--- 112
           GCRKN R      K+  +N+ P          +     + S  + G  IDLA+V+AN   
Sbjct: 61  GCRKNRRGN----KTLDHNNNPIGHSYDPRIRTSSASSSSSVVSDGPHIDLALVYANFLN 116

Query: 113 ----------SSTPDNVVQNDDFNVHN--------VMG----------NGDLNILGEFPQ 144
                     S+ PD V    D ++ N        V+G           G LN+  + PQ
Sbjct: 117 QKPNSEARVESTNPDQVQTVFDPSLENNSRLSNTVVVGPNTLPEELGLTGCLNLPEQQPQ 176

Query: 145 V-------------FGQLQEEEDRRVQDFLEDDMVNAHG------LQALLGDEIVDH-QV 184
                         +G+    +    +D ++    N  G      L  L G+E V H   
Sbjct: 177 THSSEANNNHNQMCYGEFNTMQTLHQKDGIDQQCSNHGGGAMNFELPPLPGEEEVSHDHH 236

Query: 185 ALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLISDNWTSFDLPGFELYSR 244
            +WS+   +E + N       FQ+        D      A+L+  NW+SFDLP    +SR
Sbjct: 237 MMWSN---SEMMIN---HHHAFQVTQPPLLGPDVH---DADLLIGNWSSFDLPRDASFSR 287

Query: 245 P 245
           P
Sbjct: 288 P 288

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	245
TAIR|locus:2027027	260	AT1G21340 [Arabidopsis thalian	0.930	0.876	0.397	1.9e-35
TAIR|locus:2079954	247	AT3G52440 [Arabidopsis thalian	0.865	0.858	0.393	5.2e-33
TAIR|locus:2159275	307	OBP4 "OBF binding protein 4" [	0.412	0.328	0.554	3.3e-30
TAIR|locus:2144030	257	TMO6 "TARGET OF MONOPTEROS 6"	0.567	0.540	0.448	9.1e-29
TAIR|locus:2019499	352	AT1G64620 [Arabidopsis thalian	0.624	0.434	0.435	2.4e-28
TAIR|locus:2056588	288	AT2G28510 [Arabidopsis thalian	0.4	0.340	0.594	2.4e-28
TAIR|locus:2181773	399	AT5G02460 [Arabidopsis thalian	0.265	0.162	0.738	2.5e-28
TAIR|locus:2134981	342	AT4G24060 [Arabidopsis thalian	0.375	0.269	0.597	5e-28
TAIR|locus:2039959	369	DAG2 "DOF AFFECTING GERMINATIO	0.277	0.184	0.728	1.1e-27
TAIR|locus:2170753	372	HCA2 "HIGH CAMBIAL ACTIVITY2"	0.383	0.252	0.542	9.4e-27

TAIR|locus:2027027 AT1G21340 [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 1.9e-35, P = 1.9e-35
 Identities = 97/244 (39%), Positives = 129/244 (52%)

Query:     3 KKWKPDVE----TAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPV 58
             +KWK   E    TAP+CPRCAS NTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRN+PV
Sbjct:    24 EKWKLSYEQEAITAPACPRCASSNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNIPV 83

Query:    59 GGGCRKNGRAK-SSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSSTPD 117
             GGGCRK  R++ +S ++   N +RP    + D  D   S+P G SDIDLA VFA   T D
Sbjct:    84 GGGCRKRSRSRQNSHKRFGRNENRPDGLINQD--DGFQSSPPG-SDIDLAAVFAQYVT-D 139

Query:   118 NVVQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHGLQALLGD 177
                 + D    +   +           +   + +E D  +  + E + +     Q    D
Sbjct:   140 RSPSSTDNTTGSDQDSPITTTTHALESLSWDICQETDVDLGFYGEFNNLT----QKTKED 195

Query:   178 EIVDHQVALWSDQAETETLPNFTWQRAMFQLQDFDSFPADDQLKASANLI--SDNWTSFD 235
             + V  Q  L  D+ E          + + ++ +       DQL +  + +   DNW+S D
Sbjct:   196 QEVFGQF-LQEDREEIFEFQGLLDDKEIQEILECSFSEEPDQLVSQGSFMINGDNWSSTD 254

Query:   236 LPGF 239
             L  F
Sbjct:   255 LTRF 258

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:2079954 AT3G52440 [Arabidopsis thaliana (taxid:3702)]

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 98/249 (39%), Positives = 130/249 (52%)

Query:     5 WKPDV----ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
             W+P+     E  PSCPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWTKGGSLRNVPVGG
Sbjct:    13 WRPNANANAEITPSCPRCGSSNTKFCYYNNYSLTQPRYFCKGCRRYWTKGGSLRNVPVGG 72

Query:    61 GCRKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGS-DIDLAVVFANSSTP--- 116
             GCRK+ R KSS      NN +   + +S +       P GGS  IDLA+V+AN   P   
Sbjct:    73 GCRKSRRPKSSSG----NNTKTSLTANSGN-------PGGGSPSIDLALVYANFLNPKPD 121

Query:   117 DNVVQND------DFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLEDDMVNAHG 170
             ++++Q +      DF V N  G   ++         G   +     V+  +E+   N  G
Sbjct:   122 ESILQENCDLATTDFLVDNPTGTS-MDPSWSMDINDGH-HDHYINPVEHIVEECGYN--G 177

Query:   171 LQALLGDEIVDHQV-ALWSDQ---AETETLPNFTWQRAMFQLQDFDSFPADDQLKASANL 226
             L    G+E++      +WSD             T  +A+ +      F   D+   S NL
Sbjct:   178 LPPFPGEELLSLDTNGVWSDALLIGHNHVDVGVTPVQAVHE--PVVHFA--DESNDSTNL 233

Query:   227 ISDNWTSFD 235
             +  +W+ FD
Sbjct:   234 LFGSWSPFD 242

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

 Score = 312 (114.9 bits), Expect = 3.3e-30, Sum P(2) = 3.3e-30
 Identities = 56/101 (55%), Positives = 71/101 (70%)

Query:    15 CPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSSRRK 74
             CPRC S NTKFCYYNNY+LSQPR+FCK CRRYWTKGG LRNVPVGGGCRK  R+K+ +  
Sbjct:    53 CPRCNSLNTKFCYYNNYNLSQPRHFCKNCRRYWTKGGVLRNVPVGGGCRKAKRSKTKQVP 112

Query:    75 SPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSST 115
             S  + D+P  +    H ++  ST +  S    ++  +NS+T
Sbjct:   113 SSSSADKPTTTQDDHHVEEKSSTGSHSSSESSSLTASNSTT 153

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 = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 66/147 (44%), Positives = 87/147 (59%)

Query:    10 ETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAK 69
             E A  CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWTKGG+LRN+PVGGGCRKN R+ 
Sbjct:    52 ELALRCPRCDSTNTKFCYYNNYSLTQPRYFCKSCRRYWTKGGTLRNIPVGGGCRKNKRST 111

Query:    70 SSRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFA--NSSTPDNVVQNDDFNV 127
             SS  +S      P +      +    +  +    IDL++ FA  N   P +  Q      
Sbjct:   112 SSAARSLRTTPEPASHDGKVFSAAGFNGYSNNEHIDLSLAFALLNKQHPGSSSQ---LGF 168

Query:   128 HNVMGNGDLNILGEFPQVFGQLQEEED 154
             H+ +G+   +   +   +FG  Q++E+
Sbjct:   169 HSELGSSHQS---DMEGMFGTSQQKEN 192

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

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 71/163 (43%), Positives = 92/163 (56%)

Query:     1 MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGG 60
             +E+K +P+ + A +CPRC S NTKFCYYNNYSL+QPRYFCK CRRYWT GGSLRN+PVGG
Sbjct:    37 VERKARPEKDQALNCPRCNSLNTKFCYYNNYSLTQPRYFCKDCRRYWTAGGSLRNIPVGG 96

Query:    61 GCRKNGRAKS-SRRKSPFNNDRPKASCSSDHTDDAVSTPNGGSDIDLAVVFANSSTPDNV 119
             G RKN R+ S S   SP ++   K    +++       P+    I  A   A +   D  
Sbjct:    97 GVRKNKRSSSNSSSSSPSSSSSSKKPLFANNNTPTPPLPHLNPKIGEA---AATKVQDLT 153

Query:   120 VQNDDFNVHNVMGNGDLNILGEFPQVFGQLQEEEDRRVQDFLE 162
                   N H V    DLN+   F Q FG +       + +FL+
Sbjct:   154 FSQGFGNAHEVK---DLNLA--FSQGFG-IGHNHHSSIPEFLQ 190

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 = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 63/106 (59%), Positives = 74/106 (69%)

Query:    12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKSS 71
             A +CPRC SPNTKFCYYNNYSLSQPRYFCK CRRYWTKGG+LRNVPVGGGCR+N R+ SS
Sbjct:    47 AQNCPRCESPNTKFCYYNNYSLSQPRYFCKSCRRYWTKGGTLRNVPVGGGCRRNKRSSSS 106

Query:    72 RRKSPFNNDRPKASCSSDHTDDAVST---PNG-GSD--IDLAVVFA 111
                   NN+    +  +D   + + T   P+  G D  IDL + FA
Sbjct:   107 AFSK--NNNNKSINFHTDPLQNPLITGMPPSSFGYDHSIDLNLAFA 150

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

 Score = 286 (105.7 bits), Expect = 2.5e-28, Sum P(2) = 2.5e-28
 Identities = 48/65 (73%), Positives = 56/65 (86%)

Query:     7 PDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNG 66
             P  ETA  CPRC S NTKFCY+NNYSL+QPR+FCK CRRYWT+GG+LR+VPVGGGCR+N 
Sbjct:    89 PLPETALKCPRCDSTNTKFCYFNNYSLTQPRHFCKACRRYWTRGGALRSVPVGGGCRRNK 148

Query:    67 RAKSS 71
             R K+S
Sbjct:   149 RTKNS 153

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

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 55/92 (59%), Positives = 66/92 (71%)

Query:     2 EKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGG 61
             E+K +P+ + A +CPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWT+GGSLRN+PVGGG
Sbjct:    42 ERKARPEKDQAVNCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNIPVGGG 101

Query:    62 CRKNGRAKSSRRKSPFNNDRPKASCSSDHTDD 93
              RKN R+ SS      N+       +  H  D
Sbjct:   102 SRKNKRSHSSSSDISNNHSDSTQPATKKHLSD 133

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 = 288 (106.4 bits), Expect = 1.1e-27, Sum P(2) = 1.1e-27
 Identities = 51/70 (72%), Positives = 58/70 (82%)

Query:     2 EKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGG 61
             E+K +P  +   +CPRC S NTKFCYYNNYSL+QPRYFCKGCRRYWT+GGSLRNVPVGG 
Sbjct:    71 ERKARPQEKL--NCPRCNSTNTKFCYYNNYSLTQPRYFCKGCRRYWTEGGSLRNVPVGGS 128

Query:    62 CRKNGRAKSS 71
              RKN R+ SS
Sbjct:   129 SRKNKRSSSS 138

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

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 51/94 (54%), Positives = 68/94 (72%)

Query:     3 KKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGC 62
             ++ +P  +    CPRC S +TKFCYYNNYSLSQPRYFCK CRRYWTKGG+LRN+PVGGGC
Sbjct:    63 RRLRPPHDHPQKCPRCESTHTKFCYYNNYSLSQPRYFCKTCRRYWTKGGTLRNIPVGGGC 122

Query:    63 RKNGRAKSSRRKSPFNNDRPKASCSSDHTDDAVS 96
             RKN +  SS   S  ++ +  ++  + +T D ++
Sbjct:   123 RKNKKPSSSNSSSSTSSGKKPSNIVTANTSDLMA 156

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

---

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: GSVIVG00014273001 SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; Flags- Fragment; (356 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	245
pfam02701	63	pfam02701, zf-Dof, Dof domain, zinc finger	1e-39

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

 Score =  131 bits (330), Expect = 1e-39
 Identities = 45/57 (78%), Positives = 49/57 (85%)

Query: 14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKS 70
           CPRC S NTKFCYYNNY+L+QPRYFCK CRRYWT GG+LRNVPVGGG RKN R+ S
Sbjct: 7  KCPRCDSMNTKFCYYNNYNLNQPRYFCKNCRRYWTAGGALRNVPVGGGRRKNKRSSS 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	245
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	100.0
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	94.08
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	93.51
COG3677	129	Transposase and inactivated derivatives [DNA repli	93.21
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	91.26
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	89.17
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	86.39
cd00202	54	ZnF_GATA Zinc finger DNA binding domain; binds spe	83.06
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	82.52
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	80.19

>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=100.00  E-value=1.2e-38  Score=235.67  Aligned_cols=62  Identities=77%  Similarity=1.535  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCCceeeeecccCCCCCcccccccccccccCCccccccCCCCccCCCCCCC
Q 025998            9 VETAPSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPVGGGCRKNGRAKS   70 (245)
Q Consensus         9 ~e~~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPVGgG~RKnk~s~s   70 (245)
                      +++.++||||+|.+|||||||||+++||||||++|+||||+||+||||||||||||+|+++|
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            56789999999999999999999999999999999999999999999999999999998875

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

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

Probab=94.08  E-value=0.051  Score=37.08  Aligned_cols=28  Identities=39%  Similarity=0.893  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCCceeeeecccCCCCCccccccccc
Q 025998           12 APSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRR   45 (245)
Q Consensus        12 ~~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrR   45 (245)
                      +..||+|.+.  +...+.+    ..+|.|++|++
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            3679999998  6666665    78999999985

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

>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit

Probab=93.51  E-value=0.029  Score=47.13  Aligned_cols=34  Identities=26%  Similarity=0.791  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCCceeeeeccc--CCCCCccccccccccc
Q 025998           12 APSCPRCASPNTKFCYYNNY--SLSQPRYFCKGCRRYW   47 (245)
Q Consensus        12 ~~~CPRC~S~nTKFcYyNNy--~~~QPR~fCk~CrRyW   47 (245)
                      ...||||.|.+|+..  +.+  +.++.-|.|++|+.=+
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            369999999999965  555  4457779999998643

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=93.21  E-value=0.064  Score=44.15  Aligned_cols=35  Identities=34%  Similarity=0.704  Sum_probs=28.0

Q ss_pred             CCCCCCCCCCceeeeecccCCCCCccccccccccccc
Q 025998           13 PSCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTK   49 (245)
Q Consensus        13 ~~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~   49 (245)
                      ..||+|.+.+  +-=++-+.....||.|++|++-|+.
T Consensus        31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~   65 (129)
T COG3677          31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV   65 (129)
T ss_pred             CcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence            6899999999  3334555555999999999999874

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

Probab=91.26  E-value=0.13  Score=34.59  Aligned_cols=31  Identities=45%  Similarity=0.819  Sum_probs=21.7

Q ss_pred             CCCCCCCCCCCceeeeecccCCC-CCcccccccc
Q 025998           12 APSCPRCASPNTKFCYYNNYSLS-QPRYFCKGCR   44 (245)
Q Consensus        12 ~~~CPRC~S~nTKFcYyNNy~~~-QPR~fCk~Cr   44 (245)
                      .+.||+|.|.+.  -|=|-.+.. ..||+|++|+
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            468999999871  123444433 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=89.17  E-value=0.46  Score=32.10  Aligned_cols=37  Identities=27%  Similarity=0.815  Sum_probs=27.9

Q ss_pred             CCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 025998           13 PSCPRCASPNTKFCYYNNYSLSQP---RYFCKGCRRYWTK   49 (245)
Q Consensus        13 ~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRyWT~   49 (245)
                      .+||+|...+.-|-..+-.+...|   -|.|.+|...|..
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            379999977777666666655555   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=86.39  E-value=0.59  Score=31.33  Aligned_cols=35  Identities=29%  Similarity=0.811  Sum_probs=23.9

Q ss_pred             CCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 025998           14 SCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWT   48 (245)
Q Consensus        14 ~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT   48 (245)
                      +||.|...+.-|=-.+..+..-|-   |.|.+|..-|+
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            699999987666555665555553   89999999885

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>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=83.06  E-value=1  Score=32.27  Aligned_cols=42  Identities=26%  Similarity=0.651  Sum_probs=29.4

Q ss_pred             CCCCCCCCCceeeeecccCCCCCcccccccccccccCCccccccC
Q 025998           14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRNVPV   58 (245)
Q Consensus        14 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRnVPV   58 (245)
                      .|-.|....|..=.-.   ...+..+|-+|.-||.+.|..|.+-.
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            3777888777422221   24677899999999999997665543

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=82.52  E-value=0.38  Score=32.06  Aligned_cols=37  Identities=24%  Similarity=0.588  Sum_probs=27.2

Q ss_pred             CCCCCCCCCceeeeecccCCCCCcccccccccccccCCcccc
Q 025998           14 SCPRCASPNTKFCYYNNYSLSQPRYFCKGCRRYWTKGGSLRN   55 (245)
Q Consensus        14 ~CPRC~S~nTKFcYyNNy~~~QPR~fCk~CrRyWT~GGtLRn   55 (245)
                      +||+|...-...-+     ..-+-+.|.+|.-.|=..|.+..
T Consensus         1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G~W~d~~el~~   37 (41)
T PF13453_consen    1 KCPRCGTELEPVRL-----GDVEIDVCPSCGGIWFDAGELEK   37 (41)
T ss_pred             CcCCCCcccceEEE-----CCEEEEECCCCCeEEccHHHHHH
Confidence            69999985554444     23566889999999988776654

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=80.19  E-value=2.8  Score=32.16  Aligned_cols=39  Identities=21%  Similarity=0.652  Sum_probs=28.4

Q ss_pred             CCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccC
Q 025998           12 APSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTKG   50 (245)
Q Consensus        12 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~G   50 (245)
                      ...||+|...+.-|=..+-.+...|-   |.|..|+-.|+.+
T Consensus        62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~  103 (104)
T TIGR01384        62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY  103 (104)
T ss_pred             cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence            57999998776665555555444343   9999999999875

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

---

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	245
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	92.44
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	82.75
1tfi_A	50	Transcriptional elongation factor SII; transcripti	82.49

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

Probab=92.44  E-value=0.09  Score=36.05  Aligned_cols=49  Identities=24%  Similarity=0.554  Sum_probs=32.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCceeeeecccCCCCC---ccccccccccccc
Q 025998            1 MEKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQP---RYFCKGCRRYWTK   49 (245)
Q Consensus         1 m~~~~~~~~e~~~~CPRC~S~nTKFcYyNNy~~~QP---R~fCk~CrRyWT~   49 (245)
                      +|..|+..+....+||+|...+..|--.+-.+...|   .|.|..|.--|+.
T Consensus         4 Ie~~~~~~~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A            4 MEQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             CCCCCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             hhhhhhcCCceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            455666655556799999984443333333333344   3999999999976

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

Probab=82.75  E-value=1.4  Score=34.01  Aligned_cols=39  Identities=21%  Similarity=0.473  Sum_probs=25.1

Q ss_pred             CCCCCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 025998           11 TAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTK   49 (245)
Q Consensus        11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~   49 (245)
                      ...+||+|...+..|-..+-.+...|-   |.|..|.--|+.
T Consensus        71 ~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w~~  112 (113)
T 3h0g_I           71 SDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAFEE  112 (113)
T ss_dssp             CCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCCCC
T ss_pred             cccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEEec
Confidence            347899999876443333333332222   889999999974

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

Probab=82.49  E-value=1.2  Score=30.44  Aligned_cols=38  Identities=21%  Similarity=0.590  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCCCceeeeecccCCCCCc---ccccccccccc
Q 025998           11 TAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWT   48 (245)
Q Consensus        11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT   48 (245)
                      ....||+|...+.-|=-.+..+...|-   |.|..|..-|.
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            346899999877766665555555553   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	245
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	89.99
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	89.01
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	88.54

>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=89.99  E-value=0.18  Score=35.63  Aligned_cols=41  Identities=20%  Similarity=0.515  Sum_probs=31.4

Q ss_pred             CCCCCCCCCCCceeeeecccCCCCCc---ccccccccccccCCc
Q 025998           12 APSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTKGGS   52 (245)
Q Consensus        12 ~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~GGt   52 (245)
                      ...||+|...+.-|=..+-.+..-|-   |.|..|.-.|+..++
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            46999999877777666665554443   899999999998544

>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=89.01  E-value=0.13  Score=34.85  Aligned_cols=48  Identities=23%  Similarity=0.556  Sum_probs=33.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCceeeeecccCCCCCc---cccccccccccc
Q 025998            2 EKKWKPDVETAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYWTK   49 (245)
Q Consensus         2 ~~~~~~~~e~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyWT~   49 (245)
                      |..++..+-....||+|...+.-|--.+-.+..-|-   |.|..|.--|..
T Consensus         5 ~~~~~~~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wre   55 (57)
T d1qypa_           5 EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             CCCCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             hhccccCCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCccee
Confidence            333444444457999999888877666666555554   899999999863

>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=88.54  E-value=0.17  Score=33.74  Aligned_cols=37  Identities=22%  Similarity=0.605  Sum_probs=30.4

Q ss_pred             CCCCCCCCCCCCceeeeecccCCCCCc---cccccccccc
Q 025998           11 TAPSCPRCASPNTKFCYYNNYSLSQPR---YFCKGCRRYW   47 (245)
Q Consensus        11 ~~~~CPRC~S~nTKFcYyNNy~~~QPR---~fCk~CrRyW   47 (245)
                      ...+||+|.+.+..|--.+..+...|-   +.|..|..-|
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            346999999998887777777777766   8999999888