Citrus Sinensis ID: 023523

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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-
Protein Sequence
MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSSHQMDAGAVDCFSE
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccEEcccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccEcccccccccccccHEEEEHHHHHHHHHHHEEEEccccccccccccccccc
Coil and Loop (DISEMBL)
matsatgmVYIRVIEDVISKVRDefvnngpgesvLNELQGIWEMKMIQAGViidrtsapkqpapggpitpvhdlnvpyegteeyetptaeilfpptplqtpiqtplpgstplpgstplpgstplpgtadnstyniptgssdyptpasdsggnteaksgngrpssymppppspwmnprpplsvdvnvayvegrdeadrgtshqpltqdfftmsagkrkredfpaqyhnggynipqqdgagdAMSEIFELEVRFLSPLLIYALLYFSksshqmdagavdcfse
Flexible Loop (DISEMBL)
matsatgmvyIRVIEDVISKVRDefvnngpgesVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGgnteaksgngrpSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDeadrgtshqpltqdffTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSSHQMDAGAVDCFSE
Low Complexity Region (SEG)
MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVpyegteeyetptaeilfpptplqtpiqtplpgstplpgstplpgstplpgtADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRpssymppppspwmnprpplsVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSSHQMDAGAVDCFSE
Disordered region (IsUnstruct)
******GMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIID*******************************************************************************************************************************************************************************Y*********DAMSEIFELEVRFLSPLLIYALLYFSK***************
Disordered Region (DISOPRED)
******G*VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVII************************************************************************************************************************************************************************************************************IY***************A**C***
Disordered Region (DISEMBL)
MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDY**************************PPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSSHQMDAGAVDCFSE
Disordered Region (DISPRO)
****ATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPK**APGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR**********************KRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSK***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSSHQMDAGAVDCFSE
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	281	2.2.26 [Sep-21-2011]
Q9USU9	369	Transcription initiation	yes	no	0.181	0.138	0.411	5e-05
Q5RCU0	376	Transcription initiation	yes	no	0.156	0.117	0.477	8e-05
P52655	376	Transcription initiation	no	no	0.156	0.117	0.477	8e-05
O08949	377	Transcription initiation	yes	no	0.185	0.137	0.446	9e-05
Q99PM3	378	Transcription initiation	yes	no	0.185	0.137	0.446	0.0001
P52654	366	Transcription initiation	yes	no	0.185	0.142	0.407	0.0001
Q9UNN4	478	TFIIA-alpha and beta-like	no	no	0.281	0.165	0.313	0.0001
Q8R4I4	468	TFIIA-alpha and beta-like	no	no	0.163	0.098	0.456	0.0003

>sp|Q9USU9|TOA1_SCHPO Transcription initiation factor IIA large subunit OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=toa1 PE=1 SV=1

 Score = 48.5 bits (114), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 30/51 (58%)

Query: 1  MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          M+ S  G VY  VI DVI+  R +F  NG  ++ L ELQ +W+ K++   V
Sbjct: 1  MSNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDV 51

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with tbp mediates transcriptional activity.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q5RCU0|TF2AA_PONAB Transcription initiation factor IIA subunit 1 OS=Pongo abelii GN=GTF2A1 PE=2 SV=1

 Score = 47.8 bits (112), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 32/44 (72%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 13 LYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Pongo abelii (taxid: 9601)

>sp|P52655|TF2AA_HUMAN Transcription initiation factor IIA subunit 1 OS=Homo sapiens GN=GTF2A1 PE=1 SV=1

 Score = 47.8 bits (112), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 32/44 (72%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 13 LYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Homo sapiens (taxid: 9606)

>sp|O08949|TF2AA_RAT Transcription initiation factor IIA subunit 1 OS=Rattus norvegicus GN=Gtf2a1 PE=2 SV=1

 Score = 47.8 bits (112), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 36/56 (64%), Gaps = 4/56 (7%)

Query: 1  MATSATG----MVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          MA SA       +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 1  MANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Rattus norvegicus (taxid: 10116)

>sp|Q99PM3|TF2AA_MOUSE Transcription initiation factor IIA subunit 1 OS=Mus musculus GN=Gtf2a1 PE=2 SV=2

 Score = 47.8 bits (112), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 36/56 (64%), Gaps = 4/56 (7%)

Query: 1  MATSATG----MVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          MA SA       +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 1  MANSANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Mus musculus (taxid: 10090)

>sp|P52654|TF2AA_DROME Transcription initiation factor IIA subunit 1 OS=Drosophila melanogaster GN=TfIIA-L PE=1 SV=2

 Score = 47.8 bits (112), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 1  MATSATGM--VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          MA   T +  VY  VIEDVI+ VRD F++ G  E VL E++ +W  K++ +  +
Sbjct: 1  MALCQTSVLKVYHAVIEDVITNVRDAFLDEGVDEQVLQEMKQVWRNKLLASKAV 54

TFIIA is a component of the transcription machinery of RNA polymerase II and plays an important role in transcriptional activation. TFIIA in a complex with TBP mediates transcriptional activity.

Drosophila melanogaster (taxid: 7227)

>sp|Q9UNN4|TF2AY_HUMAN TFIIA-alpha and beta-like factor OS=Homo sapiens GN=GTF2A1L PE=2 SV=2

 Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 7/86 (8%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPI 68
          +Y  VIEDVI  VR+ F   G  E VL +L+ +WE K++Q+    D      Q       
Sbjct: 10 LYRSVIEDVIEGVRNLFAEEGIEEQVLKDLKQLWETKVLQSKATEDFFRNSIQ------- 62

Query: 69 TPVHDLNVPYEGTEEYETPTAEILFP 94
          +P+  L +P+   +  ++ TA ++ P
Sbjct: 63 SPLFTLQLPHSLHQTLQSSTASLVIP 88

May function as a testis specific transcription factor. Binds DNA in conjunction with GTF2A2 and TBP (the TATA-binding protein) and together with GTF2A2, allows mRNA transcription.

Homo sapiens (taxid: 9606)

>sp|Q8R4I4|TF2AY_MOUSE TFIIA-alpha and beta-like factor OS=Mus musculus GN=Gtf2a1l PE=2 SV=2

 Score = 45.8 bits (107), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 28/46 (60%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIID 54
          +Y  VIEDVI  VRD F   G  E VL +L+ +WE K++Q+    D
Sbjct: 10 LYQSVIEDVIEGVRDLFAEEGIEEQVLKDLKKLWETKVLQSKATED 55

May function as a testis specific transcription factor. Binds DNA in conjunction with GTF2A2 and TBP (the TATA-binding protein) and together with GTF2A2, allows mRNA transcription.

Mus musculus (taxid: 10090)

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	281
356557404	390	PREDICTED: transcription initiation fact	0.800	0.576	0.665	2e-83
255558990	383	protein with unknown function [Ricinus c	0.768	0.563	0.691	4e-82
356550303	391	PREDICTED: transcription initiation fact	0.800	0.575	0.669	5e-82
356550305	384	PREDICTED: transcription initiation fact	0.850	0.622	0.634	8e-82
225434853	393	PREDICTED: uncharacterized protein LOC10	0.800	0.572	0.671	8e-81
224054626	409	predicted protein [Populus trichocarpa]	0.914	0.628	0.624	2e-80
356538972	392	PREDICTED: uncharacterized protein LOC10	0.800	0.573	0.65	1e-79
124360553	317	Transcription factor IIA, helical [Medic	0.800	0.709	0.651	7e-78
357454247	388	Transcription factor/ transcription init	0.797	0.577	0.653	7e-78
356542288	389	PREDICTED: transcription initiation fact	0.800	0.578	0.652	8e-78

>gi|356557404|ref|XP_003547006.1| PREDICTED: transcription initiation factor IIA large subunit-like [Glycine max]

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 169/254 (66%), Positives = 192/254 (75%), Gaps = 29/254 (11%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRT 56
           MA S T  VYI VIEDV+ KVRDEFVNNG PGE VL ELQ +WE KM+QAG +   I+R+
Sbjct: 1   MAASTTSQVYIDVIEDVMVKVRDEFVNNGGPGEEVLKELQAMWESKMMQAGAVLGPIERS 60

Query: 57  SAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGST 116
           SA K   PGGPITPVHDLNVPYEGTEEYETPTA++LFPPTPLQTPIQ             
Sbjct: 61  SAAKA-TPGGPITPVHDLNVPYEGTEEYETPTADMLFPPTPLQTPIQ------------- 106

Query: 117 PLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNP 176
                TPLPGT DNSTYNIPTG++DYP+  +D+GGN + K    RP+ YM  P SPWMN 
Sbjct: 107 -----TPLPGTGDNSTYNIPTGANDYPSSGNDTGGNADGKG--ARPAPYM-QPSSPWMNQ 158

Query: 177 RPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQD 236
           RPPL  DVNVAYVEGRDEAD+GTS+QPLTQDFFT ++GKRKR D  +QY+ GGY IPQQD
Sbjct: 159 RPPL--DVNVAYVEGRDEADKGTSNQPLTQDFFTRTSGKRKRNDLTSQYNVGGY-IPQQD 215

Query: 237 GAGDAMSEIFELEV 250
           GAGDA   +FE+EV
Sbjct: 216 GAGDAAHGVFEIEV 229

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558990|ref|XP_002520518.1| protein with unknown function [Ricinus communis] gi|223540360|gb|EEF41931.1| protein with unknown function [Ricinus communis]

 Score =  310 bits (794), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 170/246 (69%), Positives = 196/246 (79%), Gaps = 30/246 (12%)

Query: 9   VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI---IDRTSAPKQPAPG 65
           VYI VIEDV++KVRDEF+NNGPGE+VLNELQ IWE+KM+QAGVI   I+R+S  K   PG
Sbjct: 11  VYIHVIEDVVNKVRDEFINNGPGETVLNELQAIWELKMMQAGVICGPIERSSGAKT-VPG 69

Query: 66  GPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLP 125
           G ITPVHDLNVPYEGTEEYETPTAEILFPP        TPLPG+            TPLP
Sbjct: 70  GVITPVHDLNVPYEGTEEYETPTAEILFPP--------TPLPGT----------AQTPLP 111

Query: 126 GTADNST-YNIPTG-SSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVD 183
           G+ DNS+ YNIPTG +S+YPTP SDSGG+TEAK+  GRPS YM  PPSPW+N RPPL  D
Sbjct: 112 GSVDNSSMYNIPTGPTSEYPTPVSDSGGSTEAKA--GRPSPYM-QPPSPWINQRPPL--D 166

Query: 184 VNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMS 243
           VN+AYVEGR+EADRGTS+QPLTQDFFT ++GKRKREDF AQY+NGG+ IPQQDGAGD   
Sbjct: 167 VNIAYVEGREEADRGTSNQPLTQDFFTGASGKRKREDFAAQYNNGGF-IPQQDGAGDTPF 225

Query: 244 EIFELE 249
           E+ ++E
Sbjct: 226 EVLQVE 231

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550303|ref|XP_003543527.1| PREDICTED: transcription initiation factor IIA large subunit-like isoform 1 [Glycine max]

 Score =  310 bits (794), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 170/254 (66%), Positives = 190/254 (74%), Gaps = 29/254 (11%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRT 56
           MA S T  VYI VIEDV+ KVRDEFVNNG PGE VL ELQ +WE KM+QAG +   I+R+
Sbjct: 1   MAASTTSQVYIDVIEDVMVKVRDEFVNNGGPGEEVLKELQAMWESKMMQAGAVLGPIERS 60

Query: 57  SAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGST 116
           +A K P PGGPITPVHDLNVPYEGT+EYETPTA++LFPPTPLQTPIQ             
Sbjct: 61  TAAK-PTPGGPITPVHDLNVPYEGTDEYETPTADMLFPPTPLQTPIQ------------- 106

Query: 117 PLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNP 176
                TPLPGT DNSTYNIPTG SDYP+  +D+GGN + K    RP+ YM   PSPWMN 
Sbjct: 107 -----TPLPGTGDNSTYNIPTGPSDYPSSGNDTGGNADGKG--ARPAPYM-QSPSPWMNQ 158

Query: 177 RPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQD 236
           RPPL  DVNVAYVEGRDEADRGTS+QP TQDFFTM +GKRKR D  +QY+ GGY IPQQD
Sbjct: 159 RPPL--DVNVAYVEGRDEADRGTSNQPPTQDFFTMPSGKRKRNDLTSQYNAGGY-IPQQD 215

Query: 237 GAGDAMSEIFELEV 250
           GAGDA    FE+EV
Sbjct: 216 GAGDATHGDFEIEV 229

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550305|ref|XP_003543528.1| PREDICTED: transcription initiation factor IIA large subunit-like isoform 2 [Glycine max]

 Score =  309 bits (792), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 175/276 (63%), Positives = 196/276 (71%), Gaps = 37/276 (13%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRT 56
           MA S T  VYI VIEDV+ KVRDEFVNNG PGE VL ELQ +WE KM+QAG +   I+R+
Sbjct: 1   MAASTTSQVYIDVIEDVMVKVRDEFVNNGGPGEEVLKELQAMWESKMMQAGAVLGPIERS 60

Query: 57  SAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGST 116
           +A K P PGGPITPVHDLNVPYEGT+EYETPTA++LFPPTPLQTPIQ             
Sbjct: 61  TAAK-PTPGGPITPVHDLNVPYEGTDEYETPTADMLFPPTPLQTPIQ------------- 106

Query: 117 PLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNP 176
                TPLPGT DNSTYNIPTG SDYP+  +D+GGN + K    RP+ YM   PSPWMN 
Sbjct: 107 -----TPLPGTGDNSTYNIPTGPSDYPSSGNDTGGNADGKG--ARPAPYM-QSPSPWMNQ 158

Query: 177 RPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQD 236
           RPPL  DVNVAYVEGRDEADRGTS+QP TQDFFTM +GKRKR D  +QY+ GGY IPQQD
Sbjct: 159 RPPL--DVNVAYVEGRDEADRGTSNQPPTQDFFTMPSGKRKRNDLTSQYNAGGY-IPQQD 215

Query: 237 GAGDAMSEIFELEVRFLSPLLIYALLYFSKSSHQMD 272
           GAGDA    FE+E  FL       + Y SK     D
Sbjct: 216 GAGDATHGDFEIE--FLK------IAYISKGKMSAD 243

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434853|ref|XP_002282322.1| PREDICTED: uncharacterized protein LOC100241598 [Vitis vinifera] gi|297746029|emb|CBI16085.3| unnamed protein product [Vitis vinifera]

 Score =  306 bits (783), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 170/253 (67%), Positives = 187/253 (73%), Gaps = 28/253 (11%)

Query: 3   TSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRTSA 58
           +S T  VY+ VIEDVI+KVRDEFVNNG PGESVL+ELQGIWEMKM+QAGV+   I+R++A
Sbjct: 4   SSMTSTVYVSVIEDVINKVRDEFVNNGGPGESVLSELQGIWEMKMVQAGVVTGPIERSTA 63

Query: 59  PKQPAPG-GPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTP 117
           PKQ +    P  PVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPG         
Sbjct: 64  PKQTSGAPAPTPPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPG--------- 114

Query: 118 LPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPR 177
                      DNS YNIPTG ++YP  A D GG T+ KSG        P   SPWM  R
Sbjct: 115 ---------MGDNSMYNIPTGPTEYPA-AQDGGGATDMKSGRPPSYMPPP---SPWMQQR 161

Query: 178 PPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDG 237
           PPLSVDVNVAYVEGRDE DRG S QPLTQDFF MS+GKRKREDFP+QYH  GY IPQQDG
Sbjct: 162 PPLSVDVNVAYVEGRDEGDRGNSQQPLTQDFFMMSSGKRKREDFPSQYHTSGY-IPQQDG 220

Query: 238 AGDAMSEIFELEV 250
           AGD   E+FE+EV
Sbjct: 221 AGDPAPEVFEVEV 233

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054626|ref|XP_002298340.1| predicted protein [Populus trichocarpa] gi|222845598|gb|EEE83145.1| predicted protein [Populus trichocarpa]

 Score =  305 bits (780), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 178/285 (62%), Positives = 210/285 (73%), Gaps = 28/285 (9%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRT 56
           MA+SAT  VY  VIEDVI KVRDEF+NNG PGE+VL+ELQG+WE K++QAGV+   I R+
Sbjct: 1   MASSATSTVYTEVIEDVIDKVRDEFINNGGPGETVLSELQGLWEKKLMQAGVLSGPIVRS 60

Query: 57  SAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGS--TPLPG 114
           SA KQ  PGG +TPVHDLNVPYEGTEEYETPTAEILFPPTPL    QTPLPG+  TPLPG
Sbjct: 61  SANKQLVPGG-LTPVHDLNVPYEGTEEYETPTAEILFPPTPLPGSAQTPLPGNVQTPLPG 119

Query: 115 STPLPGSTPLPGTADNST-YNIPTG-SSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSP 172
           + P    TPLPG+ DNS+ YNI TG SSDYPTP SD+GG+T+ K+  GRPS +M   PSP
Sbjct: 120 NVP----TPLPGSVDNSSMYNISTGSSSDYPTPVSDAGGSTDVKA--GRPSHFM-QSPSP 172

Query: 173 WMNPRPPLSVDVN----------VAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFP 222
            M+ RPPL V+V           VAYVEGRDE DRG SHQ LTQDFF MS+GKRKR DF 
Sbjct: 173 LMHQRPPLDVNVGKVLTNKCCAFVAYVEGRDEVDRGGSHQTLTQDFF-MSSGKRKRGDFA 231

Query: 223 AQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKS 267
            +Y+NGG+ IPQQDGA D+ SE+ ++E   ++      L   S+S
Sbjct: 232 PKYNNGGF-IPQQDGAVDSASEVSQVECDTITTKNREILARVSRS 275

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538972|ref|XP_003537974.1| PREDICTED: uncharacterized protein LOC100800601 [Glycine max]

 Score =  302 bits (773), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 169/260 (65%), Positives = 192/260 (73%), Gaps = 35/260 (13%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRT 56
           MA S T  VYI+VI+DV++KVRDEFVNNG PG+ VL ELQ IWE KM+QAG I   I+R+
Sbjct: 1   MAASTTSQVYIQVIDDVMNKVRDEFVNNGGPGDEVLKELQSIWESKMMQAGAIVGPIERS 60

Query: 57  SAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGST 116
            APK P PGGPITPVHDLN+PYEGTEEYETPTAE+LFPPTPLQTP+Q             
Sbjct: 61  GAPK-PTPGGPITPVHDLNMPYEGTEEYETPTAEMLFPPTPLQTPLQ------------- 106

Query: 117 PLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWM-- 174
                TPLPGT DNS YNIPTG SDYP+  ++ G N E K   GRP  YM PPPSPW   
Sbjct: 107 -----TPLPGTVDNSMYNIPTGPSDYPSAGNEPGANNEIKG--GRPGPYMQPPPSPWTNQ 159

Query: 175 ----NPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGY 230
               N R PL  DVNVAYVEGRDEA+RG S+QPLTQDFF MS+GKRKR++  +QY+ GGY
Sbjct: 160 NQNQNQRAPL--DVNVAYVEGRDEAERGASNQPLTQDFF-MSSGKRKRDEIASQYNAGGY 216

Query: 231 NIPQQDGAGDAMSEIFELEV 250
            IPQQDGAGDA S+I E+EV
Sbjct: 217 -IPQQDGAGDAASQILEIEV 235

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|124360553|gb|ABD33143.2| Transcription factor IIA, helical [Medicago truncatula]

 Score =  296 bits (758), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 168/258 (65%), Positives = 185/258 (71%), Gaps = 33/258 (12%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG--PGESVLNELQGIWEMKMIQAGVI---IDR 55
           MA S T  VYI VIEDV+ KVRDEFVN G  PG+ VL ELQ IWE K IQAG +   I+R
Sbjct: 1   MAASTTSQVYIDVIEDVMVKVRDEFVNTGASPGDEVLRELQAIWESKCIQAGAVLGPIER 60

Query: 56  TSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGS 115
            +   +P PGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPG    PG 
Sbjct: 61  NTGVNRPMPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPG----PGE 116

Query: 116 TPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPW-- 173
           TP               YNIPTG SDY +  +D+GGN + K G     ++M PPPSPW  
Sbjct: 117 TP--------------NYNIPTGPSDY-SSGNDAGGNADVKGGR---QAFM-PPPSPWMN 157

Query: 174 MNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIP 233
           MN RPPL  DVNVAYVEGRDEADRG S+QP+TQDFFTM+ GKRKR D P  Y  GGY IP
Sbjct: 158 MNQRPPL--DVNVAYVEGRDEADRGASNQPMTQDFFTMTGGKRKRNDLPPPYDAGGY-IP 214

Query: 234 QQDGAGDAMSEIFELEVR 251
           QQDGAGDA+S  FE+E R
Sbjct: 215 QQDGAGDAVSGDFEIESR 232

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357454247|ref|XP_003597404.1| Transcription factor/ transcription initiation factor [Medicago truncatula] gi|355486452|gb|AES67655.1| Transcription factor/ transcription initiation factor [Medicago truncatula] gi|388523053|gb|AFK49588.1| unknown [Medicago truncatula]

 Score =  296 bits (758), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 168/257 (65%), Positives = 185/257 (71%), Gaps = 33/257 (12%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG--PGESVLNELQGIWEMKMIQAGVI---IDR 55
           MA S T  VYI VIEDV+ KVRDEFVN G  PG+ VL ELQ IWE K IQAG +   I+R
Sbjct: 1   MAASTTSQVYIDVIEDVMVKVRDEFVNTGASPGDEVLRELQAIWESKCIQAGAVLGPIER 60

Query: 56  TSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGS 115
            +   +P PGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPG    PG 
Sbjct: 61  NTGVNRPMPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPG----PGE 116

Query: 116 TPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPW-- 173
           TP               YNIPTG SDY +  +D+GGN + K G     ++M PPPSPW  
Sbjct: 117 TP--------------NYNIPTGPSDY-SSGNDAGGNADVKGGR---QAFM-PPPSPWMN 157

Query: 174 MNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIP 233
           MN RPPL  DVNVAYVEGRDEADRG S+QP+TQDFFTM+ GKRKR D P  Y  GGY IP
Sbjct: 158 MNQRPPL--DVNVAYVEGRDEADRGASNQPMTQDFFTMTGGKRKRNDLPPPYDAGGY-IP 214

Query: 234 QQDGAGDAMSEIFELEV 250
           QQDGAGDA+S  FE+EV
Sbjct: 215 QQDGAGDAVSGDFEIEV 231

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542288|ref|XP_003539601.1| PREDICTED: transcription initiation factor IIA large subunit-like isoform 2 [Glycine max]

 Score =  296 bits (758), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 167/256 (65%), Positives = 190/256 (74%), Gaps = 31/256 (12%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNG-PGESVLNELQGIWEMKMIQAGVI---IDRT 56
           MA S+T  VYI+VI+DV+ KVRDEFVNNG PG+ VL ELQ IWE KM+QAG I   I+R+
Sbjct: 1   MAASSTSQVYIQVIDDVMIKVRDEFVNNGGPGDEVLKELQSIWESKMLQAGAIVGPIERS 60

Query: 57  SAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGST 116
            APK P PGGPITPVHDLN+PYEGTEEYETPTAE+LFPPTPLQTP+Q             
Sbjct: 61  GAPK-PTPGGPITPVHDLNMPYEGTEEYETPTAEMLFPPTPLQTPLQ------------- 106

Query: 117 PLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPP--SPWM 174
                TPLPGT DNS YNIPTG SDYP+  ++ G N E K   GRP  YM PPP  S   
Sbjct: 107 -----TPLPGTVDNSMYNIPTGPSDYPSAGNEPGENNEIKG--GRPGPYMQPPPWTSQNQ 159

Query: 175 NPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQ 234
           N R PL  DVNVAYVEGRD A+RG S+QPLTQDFF MS+GKRKR++  +QY+ GGY IPQ
Sbjct: 160 NQRAPL--DVNVAYVEGRDAAERGASNQPLTQDFF-MSSGKRKRDEIASQYNAGGY-IPQ 215

Query: 235 QDGAGDAMSEIFELEV 250
           QDGAGDA S+IFE+EV
Sbjct: 216 QDGAGDADSQIFEIEV 231

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	281
TAIR|locus:2024977	375	AT1G07480 "AT1G07480" [Arabido	0.516	0.386	0.443	2.6e-49
TAIR|locus:2025027	375	AT1G07470 "AT1G07470" [Arabido	0.516	0.386	0.45	4.2e-49
TAIR|locus:2168464	186	AT5G59230 [Arabidopsis thalian	0.241	0.365	0.405	1e-09
UNIPROTKB|G4MXK1	407	MGG_01235 "Uncharacterized pro	0.234	0.162	0.371	2.1e-05
CGD|CAL0003530	275	orf19.2682 [Candida albicans (	0.181	0.185	0.490	6.9e-05
RGD|69246	377	Gtf2a1 "general transcription	0.177	0.132	0.44	0.00022
MGI|MGI:1933277	378	Gtf2a1 "general transcription	0.177	0.132	0.44	0.00022
UNIPROTKB|P52655	376	GTF2A1 "Transcription initiati	0.177	0.132	0.44	0.00071
POMBASE|SPBC28F2.09	369	toa1 "transcription factor TFI	0.245	0.186	0.373	0.00082

TAIR|locus:2024977 AT1G07480 "AT1G07480" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.6e-49, Sum P(2) = 2.6e-49
 Identities = 71/160 (44%), Positives = 93/160 (58%)

Query:   128 ADNST-YNIPTGSSDYPTPASDSGGNTEAKSGNGRXXXXXXXXXXXXXXXXXXXXVDVNV 186
             ADNS+ YNIPTGSSDYPTP +++G N + K+                        +DVNV
Sbjct:   112 ADNSSMYNIPTGSSDYPTPGTENGVNIDVKA--------RPSPYMPPPSPWTNPRLDVNV 163

Query:   187 AYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEI- 245
             AYV+GRDE +RG S+Q  TQD F  S+GKRKR+D    Y NGG +IPQQDGAGDA+ E  
Sbjct:   164 AYVDGRDEPERGNSNQQFTQDLFVPSSGKRKRDDSSGHYQNGG-SIPQQDGAGDAIPEAN 222

Query:   246 FELEVRFLSPLLIYALL--YFSKSSH--QMDAGAVDCFSE 281
             FE +   ++ +    +   +FS SS   Q+D    D + E
Sbjct:   223 FECDAFRITSIGDRKVPRDFFSSSSKIPQVDGPMPDPYDE 262

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

GO:0005634 "nucleus" evidence=ISM

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=ISS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

TAIR|locus:2025027 AT1G07470 "AT1G07470" [Arabidopsis thaliana (taxid:3702)]

 Score = 277 (102.6 bits), Expect = 4.2e-49, Sum P(2) = 4.2e-49
 Identities = 72/160 (45%), Positives = 91/160 (56%)

Query:   128 ADNST-YNIPTGSSDYPTPASDSGGNTEAKSGNGRXXXXXXXXXXXXXXXXXXXXVDVNV 186
             ADNS+ YNIPTGSSDYPTP +++G N + K+                        +DVNV
Sbjct:   112 ADNSSMYNIPTGSSDYPTPGTENGVNIDVKA--------RPSPYMPPPSPWTNPRLDVNV 163

Query:   187 AYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEI- 245
             AYV+GRDE +RG S+Q  TQD F  S+GKRKR+D  A Y NGG +IPQQDGA DA+ E  
Sbjct:   164 AYVDGRDEPERGNSNQQFTQDLFVPSSGKRKRDDSSAHYQNGG-SIPQQDGASDAIPEAN 222

Query:   246 FE---LEVRFLSPLLIYALLYFSKSS-HQMDAGAVDCFSE 281
             FE   L + ++    I   L  S S   Q+D    D + E
Sbjct:   223 FECAALRITYVGDRKIPRDLIGSSSKIPQVDGPMPDPYDE 262

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

GO:0005634 "nucleus" evidence=ISM

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=ISS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

TAIR|locus:2168464 AT5G59230 [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 1.0e-09, Sum P(2) = 1.0e-09
 Identities = 28/69 (40%), Positives = 40/69 (57%)

Query:     1 MATSATGMVYIRVIEDVISKVRDEFVNNGP-GESVLNELQGIWEMKMIQAGVIIDRTSAP 59
             ++TS T   Y  VI+DVI+K R + V NG   ESVL+++Q +W+ KMIQAG +       
Sbjct:     3 LSTSDTSSSYNYVIDDVINKSRCDLVYNGELDESVLSQIQSMWKTKMIQAGAMSGTIETS 62

Query:    60 KQPAPGGPI 68
                 P  P+
Sbjct:    63 SASIPTTPV 71

GO:0005634 "nucleus" evidence=ISM

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|G4MXK1 MGG_01235 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 123 (48.4 bits), Expect = 2.1e-05, P = 2.1e-05
 Identities = 26/70 (37%), Positives = 38/70 (54%)

Query:     1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPK 60
             M+ +  G VY ++I+ V+   R +F +NG GES +NELQ +W+ K+   G      S P 
Sbjct:     1 MSNAVVGTVYEQIIKGVMEASRTDFEDNGFGESEINELQQVWQQKLTTMGA----ASFPW 56

Query:    61 QPAPGGPITP 70
              P P  P  P
Sbjct:    57 DPKPDAPTPP 66

GO:0043581 "mycelium development" evidence=IEP

CGD|CAL0003530 orf19.2682 [Candida albicans (taxid:5476)]

 Score = 116 (45.9 bits), Expect = 6.9e-05, P = 6.9e-05
 Identities = 25/51 (49%), Positives = 33/51 (64%)

Query:     1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
             M+ + T  +Y  VIEDVI+  R +F NNG  ES L EL+ IW  K+ Q+GV
Sbjct:     1 MSNTETSKLYESVIEDVINDSRQDFENNGIDESTLQELRRIWCEKLTQSGV 51

GO:0005672 "transcription factor TFIIA complex" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0017025 "TBP-class protein binding" evidence=IEA

GO:0001129 "TBP-class protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" evidence=IEA

RGD|69246 Gtf2a1 "general transcription factor IIA, 1" [Rattus norvegicus (taxid:10116)]

 Score = 108 (43.1 bits), Expect = 0.00022, Sum P(2) = 0.00022
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query:     3 TSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
             T+    +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct:     7 TNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=ISO

GO:0003677 "DNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005672 "transcription factor TFIIA complex" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

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

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0017025 "TBP-class protein binding" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=ISO

MGI|MGI:1933277 Gtf2a1 "general transcription factor II A, 1" [Mus musculus (taxid:10090)]

 Score = 108 (43.1 bits), Expect = 0.00022, Sum P(2) = 0.00022
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query:     3 TSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
             T+    +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct:     7 TNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IPI

GO:0003677 "DNA binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005672 "transcription factor TFIIA complex" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0017025 "TBP-class protein binding" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=ISO

UNIPROTKB|P52655 GTF2A1 "Transcription initiation factor IIA subunit 1" [Homo sapiens (taxid:9606)]

 Score = 108 (43.1 bits), Expect = 0.00071, Sum P(2) = 0.00071
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query:     3 TSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
             T+    +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct:     7 TNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 56

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

GO:0005515 "protein binding" evidence=IPI

GO:0003713 "transcription coactivator activity" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA;TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

GO:0005672 "transcription factor TFIIA complex" evidence=IDA

GO:0017025 "TBP-class protein binding" evidence=IPI

GO:0008134 "transcription factor binding" evidence=IPI

GO:0046982 "protein heterodimerization activity" evidence=IPI

POMBASE|SPBC28F2.09 toa1 "transcription factor TFIIA complex large subunit Toa1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 109 (43.4 bits), Expect = 0.00082, Sum P(2) = 0.00082
 Identities = 28/75 (37%), Positives = 39/75 (52%)

Query:     1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPK 60
             M+ S  G VY  VI DVI+  R +F  NG  ++ L ELQ +W+ K++   V     + P 
Sbjct:     1 MSNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDV----ATFPW 56

Query:    61 QPAPGG--PITPVHD 73
               AP G  PI  + D
Sbjct:    57 AQAPVGTFPIGQLFD 71

GO:0000991 "core RNA polymerase II binding transcription factor activity" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005672 "transcription factor TFIIA complex" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISO

---

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: GSVIVG00024268001 SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (354 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	281
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	2e-27
cd07976	102	cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA	7e-17
COG5149	293	COG5149, TOA1, Transcription initiation factor IIA	2e-06

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score =  108 bits (271), Expect = 2e-27
 Identities = 63/245 (25%), Positives = 85/245 (34%), Gaps = 57/245 (23%)

Query: 9   VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDRTSAPKQPAPGGPI 68
           VY  VIEDVI+ VR++F + G  E VL +L+ +WE K+ Q+GV                 
Sbjct: 2   VYESVIEDVINDVREDFEDEGVDEQVLQDLKKLWEKKLSQSGV----------------- 44

Query: 69  TPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTA 128
                                   FP  P             PLP   P      LP   
Sbjct: 45  --AE--------------------FPWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAG- 81

Query: 129 DNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAY 188
           D   +N PTGS     PA      T A        +     P      + P+ V  N A 
Sbjct: 82  DQQQHNTPTGSPAANPPA------TFALPAGPAGPTIQ-TEPGQLYPVQVPVMVTQNPAN 134

Query: 189 VEGRDEADRGTSHQPLTQDFFTMSAGKR--------KREDFPAQY-HNGGYNIPQQDGAG 239
               D+  +  + Q L Q +   ++G+         K ++   Q   NG     Q DGAG
Sbjct: 135 S-PLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETPPQQTDGAG 193

Query: 240 DAMSE 244
           D  SE
Sbjct: 194 DDESE 198

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|199899 cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA alpha and beta subunits and similar proteins

 Score = 73.7 bits (182), Expect = 7e-17
 Identities = 23/44 (52%), Positives = 31/44 (70%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          VY  VIEDVI+ VR++F + G  ESVL EL+ +WE K+ Q+G  
Sbjct: 4  VYESVIEDVINNVREDFEDEGVDESVLQELKQLWEEKLSQSGAA 47

Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage). Length = 102

>gnl|CDD|227478 COG5149, TOA1, Transcription initiation factor IIA, large chain [Transcription]

 Score = 48.1 bits (114), Expect = 2e-06
 Identities = 21/51 (41%), Positives = 30/51 (58%)

Query: 1  MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          M+ S  G VY  VI DVI+  R +F  NG  ++ L ELQ +W+ K++   V
Sbjct: 1  MSNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDV 51

Length = 293

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	281
KOG2652	348	consensus RNA polymerase II transcription initiati	100.0
PF03153	375	TFIIA: Transcription factor IIA, alpha/beta subuni	99.96
COG5149	293	TOA1 Transcription initiation factor IIA, large ch	99.59

>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]

Probab=100.00  E-value=1.6e-34  Score=270.51  Aligned_cols=205  Identities=35%  Similarity=0.534  Sum_probs=169.3

Q ss_pred             CCCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC-CCCCCCCCCCCCCCccccccCCCC
Q 023523            1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR-TSAPKQPAPGGPITPVHDLNVPYE   79 (281)
Q Consensus         1 MSNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp-d~AP~pP~P~gpitPVhdLnvPye   79 (281)
                      |+++.|++||++||+|||++||++|+|+||||+||.|||++||+||+|+|++-++ +..+.+..|.  ....|  ++|++
T Consensus         2 ~~~~~v~kvY~~VIeDVI~~vRe~F~~~GiDeqvL~eLk~lWe~Kl~qs~~~~~~~d~~s~~~p~~--~~q~~--~~~~~   77 (348)
T KOG2652|consen    2 ASTNTVSKVYESVIEDVINNVREDFLENGIDEQVLSELKNLWETKLIQSGVATFPWDRESNQRPPP--GVQLH--HVPLQ   77 (348)
T ss_pred             CcccchHHHHHHHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHhhcccccCcccccccCCCC--ccccc--Ccccc
Confidence            6778999999999999999999999999999999999999999999999999543 3333221111  22344  56666


Q ss_pred             C-CCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCcccCCCCCCCCC--CCCCCCCCCCCC
Q 023523           80 G-TEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPG-TADNSTYNIPTGSSDYP--TPASDSGGNTEA  155 (281)
Q Consensus        80 ~-teeyetPtAemlfPPtplqtp~qtplp~~~~~~~~~~~~~~~~~~g-~~~~~myniptg~s~yp--~~~~~~g~~~~~  155 (281)
                      . +..+.+|+   +||.+++|++..++|+                  | .+..|+|||+.++++|+  +|....+.|.  
T Consensus        78 ~~~~~~~~Pa---~~~~~~q~~~~~~~l~------------------~~~~~~s~~~i~~~~t~~~~~~P~~q~~~N~--  134 (348)
T KOG2652|consen   78 SATANLATPA---VFPGAPQQTPAGVPLP------------------GLSGHLSKANIPLPSTATNGQHPSQQVNVNS--  134 (348)
T ss_pred             cccccccCCc---cccccccccCcCccCc------------------cccccccccCccccccccCCcCccccccccc--
Confidence            5 56887777   8889999999998888                  7 78899999999999998  6666666655  


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCccccceeeeecCc-----cccccCCCCCCcccceeecccccccccCCCcCCCCCCc
Q 023523          156 KSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR-----DEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGY  230 (281)
Q Consensus       156 k~~~grp~~ym~~~pspw~~~~~~l~vdvnvayvegr-----de~~rg~s~~~~tqdff~~~sgkrkr~d~~~~y~~g~~  230 (281)
                          -++.|+|.| .|.|.+.|+.-  +    ||.+|     .+..+|..+++.||+-|.-++|  |+.+-.-+|.+++ 
T Consensus       135 ----~q~~p~~~p-~s~~~~~q~s~--~----~v~~~~~ip~~~p~~~~~~~~~tqq~~~~~~g--~~pq~~~~~~~~~-  200 (348)
T KOG2652|consen  135 ----TQPVPALSP-WSLQLNTQKSQ--Q----TVLQQSAIPPSGPVDGNHNQPVTQQILVPPGG--KSPQSSFHYINLN-  200 (348)
T ss_pred             ----cCCCcCcCc-ccccccccccc--c----cccccccccccCcccccccCccccccccCCCC--CCcccccceeccC-
Confidence                577889999 99999766643  3    89999     8999999999999999988777  7888888888887 


Q ss_pred             ccccCCCCCCchhhHHH
Q 023523          231 NIPQQDGAGDAMSEIFE  247 (281)
Q Consensus       231 ~ipqqdga~d~~~~~~~  247 (281)
                       |||++|+++...++..
T Consensus       201 -~~q~~~s~nd~~~~~~  216 (348)
T KOG2652|consen  201 -IPQVDGSENDVEQIDG  216 (348)
T ss_pred             -Cccccccccccccccc
Confidence             9999999998877665

>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site

Probab=99.96  E-value=4.8e-30  Score=233.34  Aligned_cols=193  Identities=28%  Similarity=0.392  Sum_probs=44.0

Q ss_pred             HhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC-CCCCCCCCCCCCCCccccccCCCCCCCCCCC
Q 023523            8 MVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR-TSAPKQPAPGGPITPVHDLNVPYEGTEEYET   86 (281)
Q Consensus         8 kVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp-d~AP~pP~P~gpitPVhdLnvPye~teeyet   86 (281)
                      |||++||+|||++||+||+|+||||+||+|||++||+||+++||+.|+ ++.+.++.+.        +.+|...      
T Consensus         1 kvY~~VI~dVI~~vr~dF~~~Gvde~vL~eLk~~We~KL~qs~v~~~~~d~~~~~~~~~--------~~~p~~~------   66 (375)
T PF03153_consen    1 KVYESVIDDVINNVREDFEEEGVDEQVLQELKQLWESKLSQSGVADFPWDPPPAPPPPP--------PQQPQPP------   66 (375)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHH-SS--TTGGGG---------------------------
T ss_pred             CcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCccCCCCcccCCCccc--------ccCCCCc------
Confidence            799999999999999999999999999999999999999999999665 5444321111        1111111      


Q ss_pred             CCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCcccCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCC
Q 023523           87 PTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPG-TADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSY  165 (281)
Q Consensus        87 PtAemlfPPtplqtp~qtplp~~~~~~~~~~~~~~~~~~g-~~~~~myniptg~s~yp~~~~~~g~~~~~k~~~grp~~y  165 (281)
                          +.+++++.+++ +++++                  . ...+.++++|++.+.+..+......+.  +  .+++.++
T Consensus        67 ----~~~~~~~~~~~-~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~--~~~~~~i  119 (375)
T PF03153_consen   67 ----QSTPPSPSQQP-QAPQA------------------IPQGQSQQQNQPSSMSNSNPPATFSTPPG--Q--VPAPPTI  119 (375)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ----ccCCCCCCCCc-ccccc------------------cCCCCccccccccccCcCCCcccccCCCc--c--cCCCCCc
Confidence                55566666666 55555                  3 455677888888777633322222111  2  2678888


Q ss_pred             CCCCCCCCCCCCCCccccceeeeecCccccccCCCCCCcccceeeccccccc-----------ccCCCcCCCCCCc-ccc
Q 023523          166 MPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRK-----------REDFPAQYHNGGY-NIP  233 (281)
Q Consensus       166 m~~~pspw~~~~~~l~vdvnvayvegrde~~rg~s~~~~tqdff~~~sgkrk-----------r~d~~~~y~~g~~-~ip  233 (281)
                      +++ +..|++.+.+..+..+.++..++....+....+++++.|+.+.+.+++           +.....++..|.. .++
T Consensus       120 q~~-pG~~~~~~~P~~~~~~~~~~~~~~~~aqq~~~qq~~q~~g~~aa~q~~~~~qq~q~~~~~~~~~~~~~~~~~~~~~  198 (375)
T PF03153_consen  120 QQP-PGQQYQVQVPSMNNQPPGNQQIAQQPAQQRAAQQLQQPYGQPAAQQISQQQQQQQPQQQQQQQQQQQQPGQQVQQQ  198 (375)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCC-CccccCcccCCccCCcccccccccccccccccccccccccccccccCCccccccccccccccccccccCCCccCCC
Confidence            888 999999898988899999999999999999999999999999999999           6777778877775 358


Q ss_pred             cCCCCCCch
Q 023523          234 QQDGAGDAM  242 (281)
Q Consensus       234 qqdga~d~~  242 (281)
                      |.||++|..
T Consensus       199 Qtdga~d~~  207 (375)
T PF03153_consen  199 QTDGAGDSE  207 (375)
T ss_dssp             ---------
T ss_pred             cccCCCCcc
Confidence            899999985

After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.

>COG5149 TOA1 Transcription initiation factor IIA, large chain [Transcription]

Probab=99.59  E-value=1.3e-15  Score=139.86  Aligned_cols=55  Identities=38%  Similarity=0.631  Sum_probs=53.9

Q ss_pred             CCCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC
Q 023523            1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR   55 (281)
Q Consensus         1 MSNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp   55 (281)
                      |||+.|++||+.||.|||+++|+||++.|||+++|+|||.+||+||.+++|+.|+
T Consensus         1 msns~~~~vy~~vi~~vi~~~r~dfe~~gvdd~tlrelqnlwq~kl~~t~vatf~   55 (293)
T COG5149           1 MSNSIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFP   55 (293)
T ss_pred             CCcchhhHHHHHHHHHHHHHhhhHHHhcCccHHHHHHHHHHHHHhhhhheeeecc
Confidence            9999999999999999999999999999999999999999999999999999776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	281
1nvp_B	57	Human TfiiaTBPDNA COMPLEX Length = 57		2e-05
1rm1_C	286	Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex L		5e-04

>pdb|1NVP|B Chain B, Human TfiiaTBPDNA COMPLEX Length = 57

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 34/50 (68%)
Query: 3  TSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          T+    +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 6  TNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 55

>pdb|1RM1|C Chain C, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex Length = 286

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 31/51 (60%)
Query: 1  MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          M+ +    VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V
Sbjct: 1  MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKV 51

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	281
1nvp_B	57	Transcription initiation factor IIA alpha chain; t	4e-19
1nh2_B	53	Transcription initiation factor IIA large chain; t	2e-18
1rm1_C	286	Transcription initiation factor IIA large chain; y	2e-17

>1nvp_B Transcription initiation factor IIA alpha chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: a.32.1.1 Length = 57

 Score = 78.0 bits (192), Expect = 4e-19
 Identities = 22/52 (42%), Positives = 34/52 (65%)

Query: 1  MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
            T+    +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 4  ANTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 55

>1nh2_B Transcription initiation factor IIA large chain; transcription/DNA; HET: 5IU; 1.90A {Saccharomyces cerevisiae} SCOP: a.32.1.1 PDB: 1ytf_B* Length = 53

 Score = 76.0 bits (187), Expect = 2e-18
 Identities = 16/49 (32%), Positives = 29/49 (59%)

Query: 4  SATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          +    VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V 
Sbjct: 3  AEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVT 51

>1rm1_C Transcription initiation factor IIA large chain; yeast TFIIA, TBP protein, ATA-box DNA, transcription/DNA complex; 2.50A {Saccharomyces cerevisiae} Length = 286

 Score = 79.2 bits (193), Expect = 2e-17
 Identities = 26/209 (12%), Positives = 60/209 (28%), Gaps = 2/209 (0%)

Query: 1   MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI--IDRTSA 58
           M+ +    VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V         
Sbjct: 1   MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFSWDNQF 60

Query: 59  PKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPL 118
            +    G       +L  P   + E+             L           +        
Sbjct: 61  NEGNINGVQNDLNFNLATPGVNSSEFNIKEENTGNEGLILPNINSNNNIPHSGETNINTN 120

Query: 119 PGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRP 178
                    A  +T      ++D  +            + N    + +            
Sbjct: 121 TVEATNNSGATLNTNTSGNTNADVTSQPKIEVKPEIELTINNANITTVENIDDESEKKDD 180

Query: 179 PLSVDVNVAYVEGRDEADRGTSHQPLTQD 207
               +      + +++ ++        + 
Sbjct: 181 EEKEEDVEKTRKEKEQIEQVKLQAKKEKR 209

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	281
1nh2_B	53	Transcription initiation factor IIA large chain; t	99.89
1nvp_B	57	Transcription initiation factor IIA alpha chain; t	99.87
1rm1_C	286	Transcription initiation factor IIA large chain; y	99.8

>1nh2_B Transcription initiation factor IIA large chain; transcription/DNA; HET: 5IU; 1.90A {Saccharomyces cerevisiae} SCOP: a.32.1.1 PDB: 1ytf_B*

Probab=99.89  E-value=7.7e-24  Score=152.43  Aligned_cols=53  Identities=30%  Similarity=0.586  Sum_probs=45.6

Q ss_pred             CCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhccccc
Q 023523            2 ATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIID   54 (281)
Q Consensus         2 SNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaif   54 (281)
                      ||+.|++||++||+|||++||++|+++||||+||+|||++||+||+|+||+.|
T Consensus         1 sn~~v~~vY~~VI~dVI~~vr~~F~~~Gvde~vL~eLk~~We~KL~~s~va~F   53 (53)
T 1nh2_B            1 SNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTF   53 (53)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHHHHHC------
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHcCCCCC
Confidence            68899999999999999999999999999999999999999999999999865

>1nvp_B Transcription initiation factor IIA alpha chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: a.32.1.1

Probab=99.87  E-value=9.4e-23  Score=148.75  Aligned_cols=51  Identities=43%  Similarity=0.721  Sum_probs=42.8

Q ss_pred             CCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhccc
Q 023523            2 ATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI   52 (281)
Q Consensus         2 SNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAa   52 (281)
                      +|+.|++||++||+|||++||++|+++||||+||+|||++||+||+|+||+
T Consensus         5 ~~~~v~~vY~~VIedVI~~vr~~F~~~Gvde~vL~eLk~~We~KL~~s~a~   55 (57)
T 1nvp_B            5 NTNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV   55 (57)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC-----
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCC
Confidence            478899999999999999999999999999999999999999999999987

>1rm1_C Transcription initiation factor IIA large chain; yeast TFIIA, TBP protein, ATA-box DNA, transcription/DNA complex; 2.50A {Saccharomyces cerevisiae}

Probab=99.80  E-value=3e-20  Score=170.17  Aligned_cols=60  Identities=28%  Similarity=0.528  Sum_probs=55.5

Q ss_pred             CCCChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHHhcccccC-CCCCC
Q 023523            1 MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVIIDR-TSAPK   60 (281)
Q Consensus         1 MSNs~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQSgAaifp-d~AP~   60 (281)
                      |||..|++||++||+|||++||++|+++||||+||+|||++||+||+|+||++|+ ++++.
T Consensus         1 MSn~~vskvY~~VIedVI~~VR~dF~deGVDE~VL~ELk~~We~KL~qsgv~~f~~dp~~~   61 (286)
T 1rm1_C            1 MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKVTTFSWDNQFN   61 (286)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTSSCCTTGGGGC
T ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHhcCcccCCCCcCcc
Confidence            9999999999999999999999999999999999999999999999999999887 44443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	281
d1nh2b_	46	a.32.1.1 (B:) Large chain TOA1, N-terminal domain	1e-19
d1nvpb_	43	a.32.1.1 (B:) Large chain TOA1, N-terminal domain	3e-17

>d1nh2b_ a.32.1.1 (B:) Large chain TOA1, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 46

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Large chain TOA1, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 77.8 bits (192), Expect = 1e-19
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 4  SATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQ 48
          +    VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +
Sbjct: 2  AEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTE 46

>d1nvpb_ a.32.1.1 (B:) Large chain TOA1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 43

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Large chain TOA1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.6 bits (176), Expect = 3e-17
 Identities = 20/42 (47%), Positives = 29/42 (69%)

Query: 6  TGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMI 47
             +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++
Sbjct: 2  VPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLM 43

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	281
d1nh2b_	46	Large chain TOA1, N-terminal domain {Baker's yeast	99.85
d1nvpb_	43	Large chain TOA1, N-terminal domain {Human (Homo s	99.82

>d1nh2b_ a.32.1.1 (B:) Large chain TOA1, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Large chain TOA1, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=1.9e-22  Score=141.11  Aligned_cols=46  Identities=33%  Similarity=0.687  Sum_probs=44.6

Q ss_pred             CChhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHHH
Q 023523            3 TSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQ   48 (281)
Q Consensus         3 Ns~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLsQ   48 (281)
                      |+.|++||++||+|||++||+||+++||||+||+|||++||+||+|
T Consensus         1 n~~v~~vY~~VI~dVI~~vR~dF~~~Gvde~vL~eLk~~We~Kl~Q   46 (46)
T d1nh2b_           1 NAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTE   46 (46)
T ss_dssp             CHHHHHHHHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhcC
Confidence            6789999999999999999999999999999999999999999986

>d1nvpb_ a.32.1.1 (B:) Large chain TOA1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Transcription factor IIA (TFIIA), alpha-helical domain
superfamily: Transcription factor IIA (TFIIA), alpha-helical domain
family: Transcription factor IIA (TFIIA), alpha-helical domain
domain: Large chain TOA1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.4e-21  Score=133.19  Aligned_cols=43  Identities=47%  Similarity=0.784  Sum_probs=41.5

Q ss_pred             hhhHhHHHHHHHHHHhhHHHHHhCCCChHHHHHHHHHHHHHHH
Q 023523            5 ATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMI   47 (281)
Q Consensus         5 ~VskVYrsVIEDVIn~VReDFeeeGVDEqVLqELKqlWE~KLs   47 (281)
                      +|++||++||+|||++||++|+++||||+||+|||++||+||+
T Consensus         1 tV~kvY~~VIedVI~~vR~~F~~~GvDe~vL~eLk~~We~KL~   43 (43)
T d1nvpb_           1 TVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLM   43 (43)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC
Confidence            4899999999999999999999999999999999999999985