Citrus Sinensis ID: 017931

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360---
Protein Sequence
MKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEEccccEEEEEccEEEEEccEEEEEEccEEcccc
Secondary Structure Prediction (SSPRO)
ccEHEcEEEEEccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEEEccEEEEEEEEEEEEEccEEEEEEEEEEEEEc
Coil and Loop (DISEMBL)
mkmiqagviidrtsapkqpapggpitpvhdlnvpyegteeyetptaeilfpptplqtpiqtplpgstplpgstplpgstplpgtadnstyniptgssdyptpasdsggnteaksgngrpssymppppspwmnprpplsvdvnvayvegrdeadrgtshqpltqdfftmsagkrkredfpaqyhnggynipqqdgagdAMSEIFELEvsefpgrqdsvtTANREIFANLASssvkipqldgpipdpyddvlstpniynyqgvvnedynivntpapndiqastpavvtqndaaeddddeplnendddelddvdqgeelnTQHLVLAQFDKVTRTKSRWKCALKDGimhinnkdilfnkatgefdf
Flexible Loop (DISEMBL)
mkmiqagviidrtsapkqpapggpitpvhDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGgnteaksgngrpSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDeadrgtshqpltqdffTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDaaeddddeplneNDDDELDDVDQGEELNTQHLvlaqfdkvtrtkSRWKCAlkdgimhinnkdilfnkatgefdf
Low Complexity Region (SEG)
MKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVpyegteeyetptaeilfpptplqtpiqtplpgstplpgstplpgstplpgtADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRpssymppppspwmnprpplsVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQndaaeddddeplnendddelddvdqgeelNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF
Disordered region (IsUnstruct)
******************************************************************************************************************************************************************************************************************************EIFANLA***VKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNT**********************************************TQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNK*******
Disordered Region (DISOPRED)
*************************TPVHDLNVPYEGTEEYETPTAEILF*************************************************************************************************************************************************************************************************************************************************************************LNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF
Disordered Region (DISEMBL)
MKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDY**************************PPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF
Disordered Region (DISPRO)
MKMIQAGVIIDRTSAPK****GGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR**********PLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNI*********************************************EELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKMIQAGVIIDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF
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	363	2.2.26 [Sep-21-2011]
P52655	376	Transcription initiation	no	no	0.195	0.188	0.426	1e-10
Q5RCU0	376	Transcription initiation	yes	no	0.195	0.188	0.426	1e-10
O08949	377	Transcription initiation	yes	no	0.195	0.188	0.426	1e-10
Q99PM3	378	Transcription initiation	no	no	0.198	0.190	0.421	2e-10
Q54G80	310	Transcription initiation	yes	no	0.118	0.138	0.604	5e-10
Q9USU9	369	Transcription initiation	yes	no	0.369	0.363	0.333	6e-10
P52654	366	Transcription initiation	no	no	0.176	0.174	0.409	1e-09
P32773	286	Transcription initiation	yes	no	0.176	0.223	0.477	3e-09
Q8R4I4	468	TFIIA-alpha and beta-like	no	no	0.184	0.143	0.376	3e-08
Q9UNN4	478	TFIIA-alpha and beta-like	no	no	0.184	0.140	0.347	5e-07

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

 Score = 68.2 bits (165), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 54/75 (72%), Gaps = 4/75 (5%)

Query: 291 AEDD--DDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHIN 348
           AED   ++EPLN  DD  + D +  E  +T+++V+ Q+DK+ R+K++WK  LKDGIM++N
Sbjct: 304 AEDGQVEEEPLNSEDD--VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLN 361

Query: 349 NKDILFNKATGEFDF 363
            +D +F+KA G+ ++
Sbjct: 362 GRDYIFSKAIGDAEW 376

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

 Score = 67.8 bits (164), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 54/75 (72%), Gaps = 4/75 (5%)

Query: 291 AEDD--DDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHIN 348
           AED   ++EPLN  DD  + D +  E  +T+++V+ Q+DK+ R+K++WK  LKDGIM++N
Sbjct: 304 AEDGQVEEEPLNSEDD--VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLN 361

Query: 349 NKDILFNKATGEFDF 363
            +D +F+KA G+ ++
Sbjct: 362 GRDYIFSKAIGDAEW 376

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

 Score = 67.8 bits (164), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 54/75 (72%), Gaps = 4/75 (5%)

Query: 291 AEDD--DDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHIN 348
           AED   ++EPLN  DD  + D +  E  +T+++V+ Q+DK+ R+K++WK  LKDGIM++N
Sbjct: 305 AEDGQVEEEPLNSEDD--VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLN 362

Query: 349 NKDILFNKATGEFDF 363
            +D +F+KA G+ ++
Sbjct: 363 GRDYIFSKAIGDAEW 377

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 = 67.4 bits (163), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 54/76 (71%), Gaps = 4/76 (5%)

Query: 290 AAEDD--DDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHI 347
            AED   ++EPLN  DD  + D +  E  +T+++V+ Q+DK+ R+K++WK  LKDGIM++
Sbjct: 305 GAEDGQVEEEPLNSEDD--VSDEEGQELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNL 362

Query: 348 NNKDILFNKATGEFDF 363
           N +D +F+KA G+ ++
Sbjct: 363 NGRDYIFSKAIGDAEW 378

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|Q54G80|TF2AA_DICDI Transcription initiation factor IIA subunit 1 OS=Dictyostelium discoideum GN=gtf2a1 PE=3 SV=1

 Score = 65.9 bits (159), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 33/43 (76%)

Query: 319 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEF 361
           +H VL Q++KV+R K++ KC  KDGIMH+N KD LFNKA GE 
Sbjct: 265 EHFVLCQYEKVSRIKNKRKCNFKDGIMHLNGKDTLFNKANGEM 307

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.

Dictyostelium discoideum (taxid: 44689)

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

 Score = 65.5 bits (158), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 48/144 (33%), Positives = 69/144 (47%), Gaps = 10/144 (6%)

Query: 229 ASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNE--DYNIVNTPAPNDIQASTPAVVT 286
           A+S   +PQ DG I D  DD  S  N  + +  + +  D  I      N I      +  
Sbjct: 226 ANSRNDVPQTDGAIHD-LDDAGSPSNFESNRFAIAQKADAEIYEVLKKNRILQIDGTIED 284

Query: 287 QNDAAEDDDDEPLNENDDDELDDVDQGEELNT-------QHLVLAQFDKVTRTKSRWKCA 339
             D  +   D P +E  + +LDD D  E   T       Q +VL  +DKV   K++WKC 
Sbjct: 285 NEDEKKPPVDTPSDEAINSDLDDPDSDEAPETEEGSDIGQAIVLCLYDKVNHHKNKWKCV 344

Query: 340 LKDGIMHINNKDILFNKATGEFDF 363
            +DG++ +N KD LF KA GEF++
Sbjct: 345 FRDGVVGVNGKDYLFFKANGEFEW 368

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

 Score = 64.3 bits (155), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 46/66 (69%), Gaps = 2/66 (3%)

Query: 298 PLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKA 357
           PLN  DD  + D D  E  +T ++++ Q+DK+TR++++WK  LKDGIM++  KD +F K+
Sbjct: 303 PLNSEDD--VTDEDSAEMFDTDNVIVCQYDKITRSRNKWKFYLKDGIMNMRGKDYVFQKS 360

Query: 358 TGEFDF 363
            G+ ++
Sbjct: 361 NGDAEW 366

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|P32773|TOA1_YEAST Transcription initiation factor IIA large subunit OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TOA1 PE=1 SV=1

 Score = 63.2 bits (152), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/67 (47%), Positives = 47/67 (70%), Gaps = 3/67 (4%)

Query: 298 PLNENDDDELDDVDQGEELN-TQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNK 356
            L+++DDD L  + +GEE    ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F K
Sbjct: 221 ELDDSDDDYL--ISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQK 278

Query: 357 ATGEFDF 363
           A  E ++
Sbjct: 279 AQVEAEW 285

TFIIA is a component of the transcription machinery of RNA polymerase II and implicated in the regulation of basal transcription. Interacts with TBP (the TATA-binding protein).

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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

 Score = 60.1 bits (144), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 47/69 (68%), Gaps = 2/69 (2%)

Query: 295 DDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILF 354
           +++PLN  DD  + + D  +  +T+++++ Q+DK+ R+K+RWK  LKDG+M    +D +F
Sbjct: 402 EEDPLNSGDD--VSEQDVPDLFDTENVIVCQYDKIHRSKNRWKFYLKDGVMCFGGRDYVF 459

Query: 355 NKATGEFDF 363
            KA GE ++
Sbjct: 460 AKAIGEAEW 468

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)

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

 Score = 55.8 bits (133), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 295 DDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILF 354
           +++PLN  DD  + + D  +  +T ++++ Q+DK+ R+K++WK  LKDG+M    +D +F
Sbjct: 412 EEDPLNSGDD--VSEQDVPDLFDTDNVIVCQYDKIHRSKNKWKFYLKDGVMCFGGRDYVF 469

Query: 355 NKATGEFDF 363
            KA G+ ++
Sbjct: 470 AKAIGDAEW 478

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)

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	363
225434853	393	PREDICTED: uncharacterized protein LOC10	0.936	0.865	0.716	1e-131
224054626	409	predicted protein [Populus trichocarpa]	0.950	0.843	0.692	1e-125
255558990	383	protein with unknown function [Ricinus c	0.911	0.864	0.686	1e-123
449450764	402	PREDICTED: transcription initiation fact	0.931	0.840	0.639	1e-117
356550303	391	PREDICTED: transcription initiation fact	0.920	0.854	0.652	1e-117
356557404	390	PREDICTED: transcription initiation fact	0.925	0.861	0.646	1e-116
224104389	401	predicted protein [Populus trichocarpa]	0.939	0.850	0.662	1e-115
356550305	384	PREDICTED: transcription initiation fact	0.911	0.861	0.643	1e-114
356538972	392	PREDICTED: uncharacterized protein LOC10	0.920	0.852	0.658	1e-112
356542286	382	PREDICTED: transcription initiation fact	0.906	0.861	0.645	1e-108

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

 Score =  474 bits (1220), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 266/371 (71%), Positives = 288/371 (77%), Gaps = 31/371 (8%)

Query: 1   MKMIQAGVI---IDRTSAPKQPAPG-GPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQ 56
           MKM+QAGV+   I+R++APKQ +    P  PVHDLNVPYEGTEEYETPTAEILFPPTPLQ
Sbjct: 46  MKMVQAGVVTGPIERSTAPKQTSGAPAPTPPVHDLNVPYEGTEEYETPTAEILFPPTPLQ 105

Query: 57  TPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGN 116
           TPIQTPLPG                    DNS YNIPTG ++YP  A D GG T+ KSG 
Sbjct: 106 TPIQTPLPG------------------MGDNSMYNIPTGPTEYPA-AQDGGGATDMKSGR 146

Query: 117 GRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKRE 176
                  P   SPWM  RPPLSVDVNVAYVEGRDE DRG S QPLTQDFF MS+GKRKRE
Sbjct: 147 PPSYMPPP---SPWMQQRPPLSVDVNVAYVEGRDEGDRGNSQQPLTQDFFMMSSGKRKRE 203

Query: 177 DFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGR---QDSVTTANREIFANLASSSV 233
           DFP+QYH  GY IPQQDGAGD   E+FE+EVS+        D +T ANREIF  +A S V
Sbjct: 204 DFPSQYHTSGY-IPQQDGAGDPAPEVFEVEVSQGSNSIKGHDILTKANREIFPQVAGSYV 262

Query: 234 KIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAED 293
           +IPQLDGPIPDPY+DVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQA TPAV  QND  +D
Sbjct: 263 RIPQLDGPIPDPYEDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQAGTPAVGIQNDVGDD 322

Query: 294 DDDE-PLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDI 352
           DDDE PLNENDDD+LDDV+QGEELNTQHLVLAQFDKVTRTKS+WKC LKDGIMHINNKDI
Sbjct: 323 DDDEPPLNENDDDDLDDVEQGEELNTQHLVLAQFDKVTRTKSKWKCTLKDGIMHINNKDI 382

Query: 353 LFNKATGEFDF 363
           LFNKA GEFDF
Sbjct: 383 LFNKANGEFDF 393

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 =  454 bits (1168), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 264/381 (69%), Positives = 303/381 (79%), Gaps = 36/381 (9%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           K++QAGV+   I R+SA KQ  PGG +TPVHDLNVPYEGTEEYETPTAEILFPPTPL   
Sbjct: 46  KLMQAGVLSGPIVRSSANKQLVPGG-LTPVHDLNVPYEGTEEYETPTAEILFPPTPLPGS 104

Query: 59  IQTPLPGS--TPLPGSTPLPGSTPLPGTADNST-YNIPTGSS-DYPTPASDSGGNTEAKS 114
            QTPLPG+  TPLPG+ P    TPLPG+ DNS+ YNI TGSS DYPTP SD+GG+T+ K+
Sbjct: 105 AQTPLPGNVQTPLPGNVP----TPLPGSVDNSSMYNISTGSSSDYPTPVSDAGGSTDVKA 160

Query: 115 GNGRPSSYMPPPPSPWMNPRPPLSVDVN----------VAYVEGRDEADRGTSHQPLTQD 164
           G  RPS +M  P SP M+ RPPL V+V           VAYVEGRDE DRG SHQ LTQD
Sbjct: 161 G--RPSHFMQSP-SPLMHQRPPLDVNVGKVLTNKCCAFVAYVEGRDEVDRGGSHQTLTQD 217

Query: 165 FFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREI 224
           FF MS+GKRKR DF  +Y+NGG+ IPQQDGA D+ SE+ ++E        D++TT NREI
Sbjct: 218 FF-MSSGKRKRGDFAPKYNNGGF-IPQQDGAVDSASEVSQVEC-------DTITTKNREI 268

Query: 225 FANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAV 284
            A ++ S VKIPQ+DGPIPDPYDD+LSTPNIYNYQGV NEDYNI NTPAPND+QASTPAV
Sbjct: 269 LARVSRSYVKIPQVDGPIPDPYDDMLSTPNIYNYQGVANEDYNIANTPAPNDLQASTPAV 328

Query: 285 VTQNDAAEDDDDEPLNENDDDELDD--VDQGEELNTQHLVLAQFDKVTRTKSRWKCALKD 342
           V+QND  +DDDDEPLNE+DDD+ D   VDQGEELNTQHL+LAQFDKVTRTKSRWKC LKD
Sbjct: 329 VSQNDDVDDDDDEPLNEDDDDDEDLDGVDQGEELNTQHLILAQFDKVTRTKSRWKCTLKD 388

Query: 343 GIMHINNKDILFNKATGEFDF 363
           G+MHINN+DILFNKATGEF+F
Sbjct: 389 GVMHINNRDILFNKATGEFEF 409

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 254/370 (68%), Positives = 295/370 (79%), Gaps = 39/370 (10%)

Query: 1   MKMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQT 57
           +KM+QAGVI   I+R+S  K   PGG ITPVHDLNVPYEGTEEYETPTAEILFPPTPL  
Sbjct: 46  LKMMQAGVICGPIERSSGAKT-VPGGVITPVHDLNVPYEGTEEYETPTAEILFPPTPL-- 102

Query: 58  PIQTPLPGSTPLPGSTPLPGSTPLPGTADNST-YNIPTG-SSDYPTPASDSGGNTEAKSG 115
                       PG+      TPLPG+ DNS+ YNIPTG +S+YPTP SDSGG+TEAK+G
Sbjct: 103 ------------PGT----AQTPLPGSVDNSSMYNIPTGPTSEYPTPVSDSGGSTEAKAG 146

Query: 116 NGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKR 175
             RPS YM PP SPW+N RPPL  DVN+AYVEGR+EADRGTS+QPLTQDFFT ++GKRKR
Sbjct: 147 --RPSPYMQPP-SPWINQRPPL--DVNIAYVEGREEADRGTSNQPLTQDFFTGASGKRKR 201

Query: 176 EDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKI 235
           EDF AQY+NGG+ IPQQDGAGD   E+ ++E       +D+V +A+ EI +++    +KI
Sbjct: 202 EDFAAQYNNGGF-IPQQDGAGDTPFEVLQVE-------RDTVISADIEILSSVTRRGLKI 253

Query: 236 PQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQN--DAAED 293
           PQLDGPIPDPYDDVLSTPNIYNYQGV NEDYNI NTPAPND+QASTPA++ QN     +D
Sbjct: 254 PQLDGPIPDPYDDVLSTPNIYNYQGVANEDYNIANTPAPNDLQASTPAIIPQNDVVDDDD 313

Query: 294 DDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDIL 353
           D+    +++DDD+LDDVDQGE++NTQHLVLAQFDKVTRTKSRWKC LKDGIMHINNKDIL
Sbjct: 314 DEPLNEDDDDDDDLDDVDQGEDMNTQHLVLAQFDKVTRTKSRWKCTLKDGIMHINNKDIL 373

Query: 354 FNKATGEFDF 363
           FNKATGEFDF
Sbjct: 374 FNKATGEFDF 383

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450764|ref|XP_004143132.1| PREDICTED: transcription initiation factor IIA large subunit-like [Cucumis sativus] gi|449496658|ref|XP_004160191.1| PREDICTED: transcription initiation factor IIA large subunit-like [Cucumis sativus]

 Score =  428 bits (1100), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 245/383 (63%), Positives = 286/383 (74%), Gaps = 45/383 (11%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           KM+QAG +   I+R SAP +P PGGPITPVHDLNVPYEGTEEYETPTA++LFPPTPLQTP
Sbjct: 44  KMMQAGAVTGPIER-SAPSKPTPGGPITPVHDLNVPYEGTEEYETPTADLLFPPTPLQTP 102

Query: 59  IQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSG---------GN 109
           IQTPLPG                  TADN+ YN+PTG SD+    +D+          GN
Sbjct: 103 IQTPLPG------------------TADNAMYNVPTGPSDHSASGTDASPAATTPGGSGN 144

Query: 110 TEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEA-DRGTS--HQPLTQDFF 166
              +  +GRP+ YM PP   WM  R P  VDVN+AYVEGR+EA DRG +  H  LTQDFF
Sbjct: 145 NNVEVRSGRPTPYMQPPS--WMGQRTP--VDVNIAYVEGREEAADRGAAGAHPSLTQDFF 200

Query: 167 TMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVS---EFPGRQDSVTTANRE 223
            M++GKRKR+DF +QY   G+ IPQQDGAGDA + +FE+E+S      GR  ++T+A   
Sbjct: 201 MMNSGKRKRDDFASQYQANGF-IPQQDGAGDAANSVFEIEISGCNSSDGRPGAITSAKSA 259

Query: 224 IFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPA 283
             +++  S +KIPQLDGP+PDPYDDVLSTPNIYNYQGV NEDYNI NTPAPND  A TPA
Sbjct: 260 TSSHIERSLLKIPQLDGPMPDPYDDVLSTPNIYNYQGVFNEDYNIANTPAPNDPPAGTPA 319

Query: 284 VVTQNDAAEDDDD-EP-LNE-NDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCAL 340
           VVTQ+D  E+++D EP LNE +DDD+LDDVDQGEEL+TQHLVLAQFDKVTRTKSRWKC L
Sbjct: 320 VVTQDDVNEEEEDSEPSLNEDDDDDDLDDVDQGEELSTQHLVLAQFDKVTRTKSRWKCTL 379

Query: 341 KDGIMHINNKDILFNKATGEFDF 363
           KDGIMHINNKDILFNKATGEFDF
Sbjct: 380 KDGIMHINNKDILFNKATGEFDF 402

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 244/374 (65%), Positives = 281/374 (75%), Gaps = 40/374 (10%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           KM+QAG +   I+R++A K P PGGPITPVHDLNVPYEGT+EYETPTA++LFPPTPLQTP
Sbjct: 46  KMMQAGAVLGPIERSTAAK-PTPGGPITPVHDLNVPYEGTDEYETPTADMLFPPTPLQTP 104

Query: 59  IQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGR 118
           IQTPLPG                  T DNSTYNIPTG SDYP+  +D+GGN + K    R
Sbjct: 105 IQTPLPG------------------TGDNSTYNIPTGPSDYPSSGNDTGGNADGKGA--R 144

Query: 119 PSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDF 178
           P+ YM  P SPWMN RPPL  DVNVAYVEGRDEADRGTS+QP TQDFFTM +GKRKR D 
Sbjct: 145 PAPYMQSP-SPWMNQRPPL--DVNVAYVEGRDEADRGTSNQPPTQDFFTMPSGKRKRNDL 201

Query: 179 PAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSV----TTANREIFANLASSSVK 234
            +QY+ GGY IPQQDGAGDA    FE+EVS   GR  S+    T +  ++ A+L  S+ +
Sbjct: 202 TSQYNAGGY-IPQQDGAGDATHGDFEIEVS---GRGISINSHHTISKGKMSADLERSTSR 257

Query: 235 IPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDD 294
           IPQLDGPIP   DDVLSTPNIYNY  V +EDYNI NTPAP ++ ASTPA++ QN+   D 
Sbjct: 258 IPQLDGPIPYDDDDVLSTPNIYNYGEVFSEDYNISNTPAPPEVPASTPALLVQNEVGNDF 317

Query: 295 D-----DEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINN 349
           D     + PLNE DDD+LDD++QGE+ NT HLVLAQFDKVTRTKSRWKC LKDGIMHINN
Sbjct: 318 DDDDDDEPPLNEEDDDDLDDMEQGEDQNTHHLVLAQFDKVTRTKSRWKCTLKDGIMHINN 377

Query: 350 KDILFNKATGEFDF 363
           KDILFNKATGEF+F
Sbjct: 378 KDILFNKATGEFEF 391

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  423 bits (1088), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 240/371 (64%), Positives = 281/371 (75%), Gaps = 35/371 (9%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           KM+QAG +   I+R+SA K   PGGPITPVHDLNVPYEGTEEYETPTA++LFPPTPLQTP
Sbjct: 46  KMMQAGAVLGPIERSSAAKA-TPGGPITPVHDLNVPYEGTEEYETPTADMLFPPTPLQTP 104

Query: 59  IQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGR 118
           IQTPLPG                  T DNSTYNIPTG++DYP+  +D+GGN + K    R
Sbjct: 105 IQTPLPG------------------TGDNSTYNIPTGANDYPSSGNDTGGNADGKGA--R 144

Query: 119 PSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDF 178
           P+ YM P  SPWMN RPPL  DVNVAYVEGRDEAD+GTS+QPLTQDFFT ++GKRKR D 
Sbjct: 145 PAPYMQPS-SPWMNQRPPL--DVNVAYVEGRDEADKGTSNQPLTQDFFTRTSGKRKRNDL 201

Query: 179 PAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANRE-IFANLASSSVKIPQ 237
            +QY+ GGY IPQQDGAGDA   +FE+EVS      +S  T ++E + A+L  S+ +IPQ
Sbjct: 202 TSQYNVGGY-IPQQDGAGDAAHGVFEIEVSGGGISINSHHTISKEKMSADLERSTSRIPQ 260

Query: 238 LDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDD-- 295
           LDGPIP   DDVLSTPNIYNY  V +EDYNI NTPAP ++ ASTPA++ QN+   D D  
Sbjct: 261 LDGPIPYD-DDVLSTPNIYNYGEVFSEDYNISNTPAPPEVPASTPALLAQNEVGNDFDDD 319

Query: 296 ---DEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDI 352
              + PLNE DDD+LDD++QG++ NT HLVLAQFDKV RTKSRWKC LKDGIMHINNKDI
Sbjct: 320 DDDEPPLNEEDDDDLDDMEQGDDQNTHHLVLAQFDKVARTKSRWKCTLKDGIMHINNKDI 379

Query: 353 LFNKATGEFDF 363
           LFNKATGEF+F
Sbjct: 380 LFNKATGEFEF 390

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224104389|ref|XP_002313420.1| predicted protein [Populus trichocarpa] gi|222849828|gb|EEE87375.1| predicted protein [Populus trichocarpa]

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 249/376 (66%), Positives = 285/376 (75%), Gaps = 35/376 (9%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTP--LQ 56
           KM+QAG I   IDR+SA K P PGGPITPVHDLNVPYEGTEEYETPTAEILFPP      
Sbjct: 47  KMMQAGAICGTIDRSSANKLPVPGGPITPVHDLNVPYEGTEEYETPTAEILFPPCANTFT 106

Query: 57  TPIQTPLPGSTPLPGSTPLPGSTPLPGTADNST-YNIPTGSSDYPTPASDSGGNTEAKSG 115
              QTPLPG+            TPLPG+ DNS+ YNIPTGSSDYPTP SD+GG+T+ K+G
Sbjct: 107 WNAQTPLPGN----------AQTPLPGSVDNSSMYNIPTGSSDYPTPVSDAGGSTDGKAG 156

Query: 116 NGRPSSYMPPPPSPWMNPRPPLSVD----VNVAYVEGRDEADRGTSHQPLTQDFFTMSAG 171
             RPS +M    S  +  +P L +       VAYVEGRDE DRGTSHQ LTQDFF M +G
Sbjct: 157 --RPSPFMV---STDLIFQPSLVLTNKCCAFVAYVEGRDEVDRGTSHQALTQDFF-MPSG 210

Query: 172 KRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASS 231
           KRKREDF  +Y+NGG+ IPQQDGAGD+ SE+ ++E++         TT N+EI A ++ S
Sbjct: 211 KRKREDFAPKYNNGGF-IPQQDGAGDSASEVSQVELN----VNSYFTTKNKEILARVSRS 265

Query: 232 SVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQ---N 288
            +KIPQ+DGPIPDPYDDVLSTPNIYNYQGV NEDYNI NTPAPND  ASTPAVV+Q    
Sbjct: 266 YLKIPQVDGPIPDPYDDVLSTPNIYNYQGVANEDYNIANTPAPNDPLASTPAVVSQNDVA 325

Query: 289 DAAEDDDDEPLNENDDDELDDVDQGEELNT-QHLVLAQFDKVTRTKSRWKCALKDGIMHI 347
           D  +DD+    +++DD++LDDVDQGEELNT QHLVLAQFDKVTRTKSRWKC LKDGIMHI
Sbjct: 326 DDDDDDEPLNEDDDDDEDLDDVDQGEELNTPQHLVLAQFDKVTRTKSRWKCILKDGIMHI 385

Query: 348 NNKDILFNKATGEFDF 363
           NNKDILFNKATGEFDF
Sbjct: 386 NNKDILFNKATGEFDF 401

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  418 bits (1075), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 238/370 (64%), Positives = 275/370 (74%), Gaps = 39/370 (10%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           KM+QAG +   I+R++A K P PGGPITPVHDLNVPYEGT+EYETPTA++LFPPTPLQTP
Sbjct: 46  KMMQAGAVLGPIERSTAAK-PTPGGPITPVHDLNVPYEGTDEYETPTADMLFPPTPLQTP 104

Query: 59  IQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGR 118
           IQTPLPG                  T DNSTYNIPTG SDYP+  +D+GGN + K    R
Sbjct: 105 IQTPLPG------------------TGDNSTYNIPTGPSDYPSSGNDTGGNADGKGA--R 144

Query: 119 PSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDF 178
           P+ YM  P SPWMN RPPL  DVNVAYVEGRDEADRGTS+QP TQDFFTM +GKRKR D 
Sbjct: 145 PAPYMQSP-SPWMNQRPPL--DVNVAYVEGRDEADRGTSNQPPTQDFFTMPSGKRKRNDL 201

Query: 179 PAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQL 238
            +QY+ GGY IPQQDGAGDA    FE+E  +          +  ++ A+L  S+ +IPQL
Sbjct: 202 TSQYNAGGY-IPQQDGAGDATHGDFEIEFLKI------AYISKGKMSADLERSTSRIPQL 254

Query: 239 DGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDD--- 295
           DGPIP   DDVLSTPNIYNY  V +EDYNI NTPAP ++ ASTPA++ QN+   D D   
Sbjct: 255 DGPIPYDDDDVLSTPNIYNYGEVFSEDYNISNTPAPPEVPASTPALLVQNEVGNDFDDDD 314

Query: 296 --DEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDIL 353
             + PLNE DDD+LDD++QGE+ NT HLVLAQFDKVTRTKSRWKC LKDGIMHINNKDIL
Sbjct: 315 DDEPPLNEEDDDDLDDMEQGEDQNTHHLVLAQFDKVTRTKSRWKCTLKDGIMHINNKDIL 374

Query: 354 FNKATGEFDF 363
           FNKATGEF+F
Sbjct: 375 FNKATGEFEF 384

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  410 bits (1053), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 247/375 (65%), Positives = 282/375 (75%), Gaps = 41/375 (10%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           KM+QAG I   I+R+ APK P PGGPITPVHDLN+PYEGTEEYETPTAE+LFPPTPLQTP
Sbjct: 46  KMMQAGAIVGPIERSGAPK-PTPGGPITPVHDLNMPYEGTEEYETPTAEMLFPPTPLQTP 104

Query: 59  IQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGR 118
           +QTPLPG                  T DNS YNIPTG SDYP+  ++ G N E K G  R
Sbjct: 105 LQTPLPG------------------TVDNSMYNIPTGPSDYPSAGNEPGANNEIKGG--R 144

Query: 119 PSSYMPPPPSPWMNP------RPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGK 172
           P  YM PPPSPW N       R PL  DVNVAYVEGRDEA+RG S+QPLTQDFF MS+GK
Sbjct: 145 PGPYMQPPPSPWTNQNQNQNQRAPL--DVNVAYVEGRDEAERGASNQPLTQDFF-MSSGK 201

Query: 173 RKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDS-VTTANREIFANLASS 231
           RKR++  +QY+ GGY IPQQDGAGDA S+I E+EV       D+  +T+  ++ A     
Sbjct: 202 RKRDEIASQYNAGGY-IPQQDGAGDAASQILEIEVYGGGMSIDAGHSTSKGKMPAQSDRP 260

Query: 232 SVKIPQLDGPIPDPYDD-VLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDA 290
           + +IPQLDGPIP  YDD VLSTPNIYNY GV NEDYNI NTPAP+++ ASTPA + QN+ 
Sbjct: 261 ASQIPQLDGPIP--YDDDVLSTPNIYNY-GVFNEDYNIANTPAPSEVPASTPAPIAQNEV 317

Query: 291 AEDDDDE--PLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHIN 348
            E+DDD+  PLNENDDD+LDD+DQGE+ NT HLVLAQFDKVTRTKSRWKC LKDGIMHIN
Sbjct: 318 DEEDDDDEPPLNENDDDDLDDLDQGEDQNTHHLVLAQFDKVTRTKSRWKCTLKDGIMHIN 377

Query: 349 NKDILFNKATGEFDF 363
           NKDILFNKATGEFDF
Sbjct: 378 NKDILFNKATGEFDF 392

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542286|ref|XP_003539600.1| PREDICTED: transcription initiation factor IIA large subunit-like isoform 1 [Glycine max]

 Score =  398 bits (1023), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 239/370 (64%), Positives = 274/370 (74%), Gaps = 41/370 (11%)

Query: 2   KMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTP 58
           KM+QAG I   I+R+ APK P PGGPITPVHDLN+PYEGTEEYETPTAE+LFPPTPLQTP
Sbjct: 46  KMLQAGAIVGPIERSGAPK-PTPGGPITPVHDLNMPYEGTEEYETPTAEMLFPPTPLQTP 104

Query: 59  IQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGR 118
           +QTPLPG                  T DNS YNIPTG SDYP+  ++ G N E K G  R
Sbjct: 105 LQTPLPG------------------TVDNSMYNIPTGPSDYPSAGNEPGENNEIKGG--R 144

Query: 119 PSSYMPPPP--SPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKRE 176
           P  YM PPP  S   N R PL  DVNVAYVEGRD A+RG S+QPLTQDFF MS+GKRKR+
Sbjct: 145 PGPYMQPPPWTSQNQNQRAPL--DVNVAYVEGRDAAERGASNQPLTQDFF-MSSGKRKRD 201

Query: 177 DFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIP 236
           +  +QY+ GGY IPQQDGAGDA S+IFE+EV  F       +T+N ++ A+    + +IP
Sbjct: 202 EIASQYNAGGY-IPQQDGAGDADSQIFEIEVWHF------FSTSNGKMPAHSDRPASQIP 254

Query: 237 QLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDD 296
           Q DGPIP   DDV+STPN+YNY GV NEDYNI NTPA +D+ ASTPA V QN+  E+DDD
Sbjct: 255 QFDGPIPYD-DDVVSTPNMYNY-GVFNEDYNIANTPASSDVPASTPAPVAQNEVDEEDDD 312

Query: 297 E--PLNENDDDELDDVD-QGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDIL 353
           +  PLNENDDD+  D   QGE+ NT HLVLAQFDKVTRTKSRWKC LKDGIMHINNKDIL
Sbjct: 313 DDEPLNENDDDDDLDDLDQGEDQNTHHLVLAQFDKVTRTKSRWKCTLKDGIMHINNKDIL 372

Query: 354 FNKATGEFDF 363
           FNKATGEF+F
Sbjct: 373 FNKATGEFEF 382

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	363
TAIR|locus:2024977	375	AT1G07480 "AT1G07480" [Arabido	0.724	0.701	0.532	2.3e-74
TAIR|locus:2025027	375	AT1G07470 "AT1G07470" [Arabido	0.721	0.698	0.530	5.9e-74
TAIR|locus:2168464	186	AT5G59230 [Arabidopsis thalian	0.129	0.252	0.553	1.1e-16
DICTYBASE|DDB_G0290327	310	gtf2a1 "transcription initiati	0.115	0.135	0.619	1.1e-08
POMBASE|SPBC28F2.09	369	toa1 "transcription factor TFI	0.123	0.121	0.488	9.2e-08
UNIPROTKB|G4MXK1	407	MGG_01235 "Uncharacterized pro	0.123	0.110	0.488	9.4e-08
ZFIN|ZDB-GENE-030131-2694	369	gtf2a1 "general transcription	0.129	0.127	0.446	1.3e-07
RGD|69246	377	Gtf2a1 "general transcription	0.129	0.124	0.446	3.7e-07
MGI|MGI:1933277	378	Gtf2a1 "general transcription	0.129	0.124	0.446	3.8e-07
UNIPROTKB|I3LE29	317	GTF2A1 "Uncharacterized protei	0.129	0.148	0.446	4.7e-07

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

 Score = 678 (243.7 bits), Expect = 2.3e-74, Sum P(2) = 2.3e-74
 Identities = 149/280 (53%), Positives = 179/280 (63%)

Query:    85 ADNST-YNIPTGSSDYPTPASDSGGNTEAKSGNGRXXXXXXXXXXXXXXXXXXXXVDVNV 143
             ADNS+ YNIPTGSSDYPTP +++G N + K+                        +DVNV
Sbjct:   112 ADNSSMYNIPTGSSDYPTPGTENGVNIDVKA--------RPSPYMPPPSPWTNPRLDVNV 163

Query:   144 AYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIF 203
             AYV+GRDE +RG S+Q  TQD F  S+GKRKR+D    Y NGG +IPQQDGAGDA+ E  
Sbjct:   164 AYVDGRDEPERGNSNQQFTQDLFVPSSGKRKRDDSSGHYQNGG-SIPQQDGAGDAIPEA- 221

Query:   204 ELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVN 263
               E   F  R  S+   +R++  +  SSS KIPQ+DGP+PDPYD++LSTPNIY+YQG  +
Sbjct:   222 NFECDAF--RITSI--GDRKVPRDFFSSSSKIPQVDGPMPDPYDEMLSTPNIYSYQGP-S 276

Query:   264 EDYNIVNTPAPNDIQASTPAVVTQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNTQHLVL 323
             E++N   TPAPN+IQ STP  V Q                             NTQHLVL
Sbjct:   277 EEFNEARTPAPNEIQTSTPVAV-QNDIIEDDEELLNEDDDDDELDDLESGEDMNTQHLVL 335

Query:   324 AQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             AQFDKVTRTKSRWKC+LKDGIMHIN+KDILFNKA GEFDF
Sbjct:   336 AQFDKVTRTKSRWKCSLKDGIMHINDKDILFNKAAGEFDF 375

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 = 674 (242.3 bits), Expect = 5.9e-74, Sum P(2) = 5.9e-74
 Identities = 149/281 (53%), Positives = 176/281 (62%)

Query:    85 ADNST-YNIPTGSSDYPTPASDSGGNTEAKSGNGRXXXXXXXXXXXXXXXXXXXXVDVNV 143
             ADNS+ YNIPTGSSDYPTP +++G N + K+                        +DVNV
Sbjct:   112 ADNSSMYNIPTGSSDYPTPGTENGVNIDVKA--------RPSPYMPPPSPWTNPRLDVNV 163

Query:   144 AYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEI- 202
             AYV+GRDE +RG S+Q  TQD F  S+GKRKR+D  A Y NGG +IPQQDGA DA+ E  
Sbjct:   164 AYVDGRDEPERGNSNQQFTQDLFVPSSGKRKRDDSSAHYQNGG-SIPQQDGASDAIPEAN 222

Query:   203 FELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVV 262
             FE                +R+I  +L  SS KIPQ+DGP+PDPYD++LSTPNIY+YQG  
Sbjct:   223 FECAALRI------TYVGDRKIPRDLIGSSSKIPQVDGPMPDPYDEMLSTPNIYSYQGP- 275

Query:   263 NEDYNIVNTPAPNDIQASTPAVVTQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNTQHLV 322
             NE++N   TPAPN+IQ STP  V                               NTQHLV
Sbjct:   276 NEEFNEARTPAPNEIQTSTPVAVPNDIIEDDEELLNEDDDDDELDDLESGEDM-NTQHLV 334

Query:   323 LAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             LAQFDKVTRTKSRWKC+LKDGIMHIN+KDILFNKATGEFDF
Sbjct:   335 LAQFDKVTRTKSRWKCSLKDGIMHINDKDILFNKATGEFDF 375

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 = 160 (61.4 bits), Expect = 1.1e-16, Sum P(2) = 1.1e-16
 Identities = 26/47 (55%), Positives = 38/47 (80%)

Query:   317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             N QHLV+ QFDKV R+K++W+C    G+M IN K++LF++ATG+F+F
Sbjct:   140 NIQHLVMCQFDKVKRSKNKWECKFNAGVMQINGKNVLFSQATGDFNF 186

GO:0005634 "nucleus" evidence=ISM

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

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

DICTYBASE|DDB_G0290327 gtf2a1 "transcription initiation factor IIA alpha chain" [Dictyostelium discoideum (taxid:44689)]

 Score = 147 (56.8 bits), Expect = 1.1e-08, Sum P(2) = 1.1e-08
 Identities = 26/42 (61%), Positives = 33/42 (78%)

Query:   319 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGE 360
             +H VL Q++KV+R K++ KC  KDGIMH+N KD LFNKA GE
Sbjct:   265 EHFVLCQYEKVSRIKNKRKCNFKDGIMHLNGKDTLFNKANGE 306

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

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

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

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

GO:0005634 "nucleus" evidence=IEA

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

 Score = 131 (51.2 bits), Expect = 9.2e-08, Sum P(2) = 9.2e-08
 Identities = 22/45 (48%), Positives = 32/45 (71%)

Query:   319 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             Q +VL  +DKV   K++WKC  +DG++ +N KD LF KA GEF++
Sbjct:   324 QAIVLCLYDKVNHHKNKWKCVFRDGVVGVNGKDYLFFKANGEFEW 368

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

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

 Score = 138 (53.6 bits), Expect = 9.4e-08, Sum P(2) = 9.4e-08
 Identities = 22/45 (48%), Positives = 35/45 (77%)

Query:   319 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             Q  +L  +DKV R K++WKC LKDG++ +N K+ +F+KATGE+++
Sbjct:   363 QQQMLCLYDKVQRVKNKWKCTLKDGVLCVNGKEYVFHKATGEYEW 407

GO:0043581 "mycelium development" evidence=IEP

ZFIN|ZDB-GENE-030131-2694 gtf2a1 "general transcription factor IIA, 1" [Danio rerio (taxid:7955)]

 Score = 133 (51.9 bits), Expect = 1.3e-07, Sum P(2) = 1.3e-07
 Identities = 21/47 (44%), Positives = 39/47 (82%)

Query:   317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct:   323 DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDFVFSKAIGDAEW 369

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

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

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

 Score = 133 (51.9 bits), Expect = 3.7e-07, Sum P(2) = 3.7e-07
 Identities = 21/47 (44%), Positives = 39/47 (82%)

Query:   317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct:   331 DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW 377

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 = 133 (51.9 bits), Expect = 3.8e-07, Sum P(2) = 3.8e-07
 Identities = 21/47 (44%), Positives = 39/47 (82%)

Query:   317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct:   332 DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW 378

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|I3LE29 GTF2A1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 133 (51.9 bits), Expect = 4.7e-07, Sum P(2) = 4.7e-07
 Identities = 21/47 (44%), Positives = 39/47 (82%)

Query:   317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
             +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct:   271 DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW 317

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

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

---

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: estExt_Genewise1_v1.C_LG_I1143 hypothetical protein (409 aa) (Populus trichocarpa)

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	363
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	1e-36
cd07976	102	cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA	7e-28
COG5149	293	COG5149, TOA1, Transcription initiation factor IIA	3e-12

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

 Score =  134 bits (340), Expect = 1e-36
 Identities = 86/336 (25%), Positives = 123/336 (36%), Gaps = 72/336 (21%)

Query: 50  FPPTPLQTPIQTPLPGSTPLPGSTPLPGSTPLPGTADNSTYNIPTGSSDYPTPASDSGGN 109
           FP  P             PLP   P      LP   D   +N PTGS     PA      
Sbjct: 47  FPWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAG-DQQQHNTPTGSPAANPPA------ 99

Query: 110 TEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMS 169
           T A        +     P      + P+ V  N A     D+  +  + Q L Q +   +
Sbjct: 100 TFALPAGPAGPTIQ-TEPGQLYPVQVPVMVTQNPANS-PLDQPAQQRALQQLQQRYGAPA 157

Query: 170 AGKR--------KREDFPAQY-HNGGYNIPQQDGAGDAMSE----------IFELEVSEF 210
           +G+         K ++   Q   NG     Q DGAGD  SE            E  +   
Sbjct: 158 SGQLPSQQQSAQKNDESQLQQQPNGETPPQQTDGAGDDESEALVRLREADGTLEQRIKGA 217

Query: 211 PGRQDSVTTANREIFANLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVN 270
            G          +     A SS +         D  D+                      
Sbjct: 218 EGGGAMK---VLKQPKKQAKSSKRRTIAQIDGIDSDDE---------------------- 252

Query: 271 TPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDDELDDV--DQGEEL-NTQHLVLAQFD 327
                            + + +DDD++ +  + DD  DDV  + GE+L +T +++L Q+D
Sbjct: 253 ----------------GDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDTDNVMLCQYD 296

Query: 328 KVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           KV R+K++WKC LKDGIM IN KD +F KATGE ++
Sbjct: 297 KVQRSKNKWKCTLKDGIMTINGKDYVFQKATGEAEW 332

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 =  104 bits (263), Expect = 7e-28
 Identities = 29/46 (63%), Positives = 39/46 (84%)

Query: 318 TQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           T+++VL Q+DKVTR K++WKC LKDGIM +N KD +F KATGEF++
Sbjct: 57  TENIVLCQYDKVTRVKNKWKCTLKDGIMTLNGKDYVFQKATGEFEW 102

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 = 66.2 bits (161), Expect = 3e-12
 Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 282 PAVVTQNDAAEDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALK 341
               T  D     D   L+++D D  D   +G + +  + +L  +DKV  +K +WKC  K
Sbjct: 215 GKPTTAKDEGMFSD---LDDSDVDSGDSEIEGTKGS-TNCMLCLYDKVNMSKGKWKCTFK 270

Query: 342 DGIMHINNKDILFNKATGEFDF 363
           DG++ INN D +FNKA GE ++
Sbjct: 271 DGVVSINNIDYVFNKAQGELEW 292

Length = 293

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	363
KOG2652	348	consensus RNA polymerase II transcription initiati	100.0
PF03153	375	TFIIA: Transcription factor IIA, alpha/beta subuni	100.0
COG5149	293	TOA1 Transcription initiation factor IIA, large ch	99.88

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

Probab=100.00  E-value=3e-56  Score=428.08  Aligned_cols=289  Identities=34%  Similarity=0.520  Sum_probs=242.0

Q ss_pred             Ccceeceee---eecCCCCCCCCCCCCCCcccccCCCCCC-cccccCCCceeccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 017931            1 MKMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEG-TEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLP   76 (363)
Q Consensus         1 ~km~q~g~i---ier~~a~~~~~p~gp~tpvhDLNvPyeg-tEEyeTPtaemLFpPtPlqtp~qTPlp~~~~~~~~~~~~   76 (363)
                      .||||+||.   ++|.+++.+ .+|+.   .|  ||||++ |.+|+||+   +||.+++|++..++||            
T Consensus        45 ~Kl~qs~~~~~~~d~~s~~~p-~~~~q---~~--~~~~~~~~~~~~~Pa---~~~~~~q~~~~~~~l~------------  103 (348)
T KOG2652|consen   45 TKLIQSGVATFPWDRESNQRP-PPGVQ---LH--HVPLQSATANLATPA---VFPGAPQQTPAGVPLP------------  103 (348)
T ss_pred             HHHHhhcccccCcccccccCC-CCccc---cc--CcccccccccccCCc---cccccccccCcCccCc------------
Confidence            389999999   999999987 55553   45  899999 79999999   8999999999999999            


Q ss_pred             CCCCCCC-CCCCCcccCCCCCCCCC--CCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCcccceeeeeecCc----
Q 017931           77 GSTPLPG-TADNSTYNIPTGSSDYP--TPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGR----  149 (363)
Q Consensus        77 ~~~~~~g-~~~~~myniptg~s~yp--~~~~d~g~~~d~k~~~grps~ym~~~pspw~~~~~~l~vdVnvAYvegr----  149 (363)
                            | .+..|||||+.+.+.|+  .|......|.      -++.|+|.| .|.|.++|+.    ++  ||.+|    
T Consensus       104 ------~~~~~~s~~~i~~~~t~~~~~~P~~q~~~N~------~q~~p~~~p-~s~~~~~q~s----~~--~v~~~~~ip  164 (348)
T KOG2652|consen  104 ------GLSGHLSKANIPLPSTATNGQHPSQQVNVNS------TQPVPALSP-WSLQLNTQKS----QQ--TVLQQSAIP  164 (348)
T ss_pred             ------cccccccccCccccccccCCcCccccccccc------cCCCcCcCc-cccccccccc----cc--ccccccccc
Confidence                  7 77899999999999998  6777766666      478899999 9999985554    33  99999    


Q ss_pred             -cccccCCCCCCCccceecccccccccccCCcCCCCCCcccccCCCCCCCcccceeeeecCCCCccccccccchhhhhhh
Q 017931          150 -DEADRGTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANL  228 (363)
Q Consensus       150 -de~drg~s~q~lTqdfftmsSGKRKRdD~~~qy~~gg~~iPQQDGa~D~~~e~~~~e~~~~~~~~~~~~~~~~~~~~~~  228 (363)
                       ..+.+|..+++.||+-|.-++|  |+.+.-.+|.+++  |||++|+++...+...       ..+.++....|...+.+
T Consensus       165 ~~~p~~~~~~~~~tqq~~~~~~g--~~pq~~~~~~~~~--~~q~~~s~nd~~~~~~-------~~~a~~~~~~~~~~~~~  233 (348)
T KOG2652|consen  165 PSGPVDGNHNQPVTQQILVPPGG--KSPQSSFHYINLN--IPQVDGSENDVEQIDG-------TDLAIHILKDRMVPRDS  233 (348)
T ss_pred             ccCcccccccCccccccccCCCC--CCcccccceeccC--Cccccccccccccccc-------ccccccccccccccccc
Confidence             8999999999999999988888  8888888888888  8999999999888765       23667888888888888


Q ss_pred             hcccccccCCCCCCCCCCCCcCCCCcccccCCcccccccccCCCCCCCcccCCCcccccCCcCCCCCCCCCCCCCCC--C
Q 017931          229 ASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLNENDDD--E  306 (363)
Q Consensus       229 ~~~~~~IPQlDGp~pdpydd~~~tpniy~yqGv~~Edyn~~~~~a~~e~~ast~~~~~~~~~~de~eEdpLNSdDDd--d  306 (363)
                      .....+|.|+||++..     +++.++|-+++  .||=||-.               ..+ ...+++|+.+|+||||  +
T Consensus       234 ~s~~~~i~qv~~~~~~-----~~Q~Dg~~~~~--eE~e~Eee---------------~~~-~~~~~dee~~n~Dd~D~~E  290 (348)
T KOG2652|consen  234 VSEKDKIAQVDLSLRK-----ILQVDGTGDTS--EEDENEEE---------------DDD-PDPDEDEELGNSDDDDGVE  290 (348)
T ss_pred             cchhhhhhhhcccccc-----eeecccccccc--cccccccc---------------ccC-cccchhhhcccccccCccc
Confidence            8899999999999984     78899999988  56444411               111 1123566777777755  5


Q ss_pred             CcccccccCCC-CCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          307 LDDVDQGEELN-TQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       307 ~dD~Dd~Ed~~-t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      ++++++++|.. |+||||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus       291 eeplnsedDvsdt~nvVvCqyDKV~RsKnKWKc~LKDGIM~ingkDY~F~KA~GeaEW  348 (348)
T KOG2652|consen  291 EEPLNSEDDVSDTQNVVVCQYDKVNRSKNKWKCYLKDGVMHINGKDYVFQKAQGEAEW  348 (348)
T ss_pred             cccccCcccccccceeEEEeeeeeccccceeeEEeecceEEeCCceeEeeecccccCC
Confidence            66666655663 8999999999999999999999999999999999999999999999

>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=100.00  E-value=2.4e-49  Score=371.69  Aligned_cols=293  Identities=33%  Similarity=0.476  Sum_probs=55.3

Q ss_pred             Ccceeceee---eecCCCCCCCCCCCCCCcccccCCCCCCcccccCCCceeccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 017931            1 MKMIQAGVI---IDRTSAPKQPAPGGPITPVHDLNVPYEGTEEYETPTAEILFPPTPLQTPIQTPLPGSTPLPGSTPLPG   77 (363)
Q Consensus         1 ~km~q~g~i---ier~~a~~~~~p~gp~tpvhDLNvPyegtEEyeTPtaemLFpPtPlqtp~qTPlp~~~~~~~~~~~~~   77 (363)
                      .||+|+||+   .+...++.++.+..|..+                    +.||+++++++ +++++             
T Consensus        37 ~KL~qs~v~~~~~d~~~~~~~~~~~~p~~~--------------------~~~~~~~~~~~-~~~~~-------------   82 (375)
T PF03153_consen   37 SKLSQSGVADFPWDPPPAPPPPPPQQPQPP--------------------QSTPPSPSQQP-QAPQA-------------   82 (375)
T ss_dssp             HHHHHH-SS--TTGGGG---------------------------------------------------------------
T ss_pred             HHHHhcCCccCCCCcccCCCcccccCCCCc--------------------ccCCCCCCCCc-ccccc-------------
Confidence            389999999   555555444233333212                    78888888888 77776             


Q ss_pred             CCCCCC-CCCCCcccCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCcccceeeeeecCccccccCC
Q 017931           78 STPLPG-TADNSTYNIPTGSSDYPTPASDSGGNTEAKSGNGRPSSYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGT  156 (363)
Q Consensus        78 ~~~~~g-~~~~~myniptg~s~yp~~~~d~g~~~d~k~~~grps~ym~~~pspw~~~~~~l~vdVnvAYvegrde~drg~  156 (363)
                           . ...+.++++|++.+.+..+......+.  +.  +++.++|++ |..|++.+.|..+..+.++..++....+..
T Consensus        83 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~iq~~-pG~~~~~~~P~~~~~~~~~~~~~~~~aqq~  152 (375)
T PF03153_consen   83 -----IPQGQSQQQNQPSSMSNSNPPATFSTPPG--QV--PAPPTIQQP-PGQQYQVQVPSMNNQPPGNQQIAQQPAQQR  152 (375)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             -----cCCCCccccccccccCcCCCcccccCCCc--cc--CCCCCccCC-CccccCcccCCccCCccccccccccccccc
Confidence                 3 455778888888777633322221111  33  578888888 999999999998999999999999999999


Q ss_pred             CCCCCccceecccccccc-----------cccCCcCCCCCCc-ccccCCCCCCCcc----cceeeeec-CC---------
Q 017931          157 SHQPLTQDFFTMSAGKRK-----------REDFPAQYHNGGY-NIPQQDGAGDAMS----EIFELEVS-EF---------  210 (363)
Q Consensus       157 s~q~lTqdfftmsSGKRK-----------RdD~~~qy~~gg~-~iPQQDGa~D~~~----e~~~~e~~-~~---------  210 (363)
                      ..+++++.|+.+++.+++           +.....++..|.. .++|.||+++...    +..+.... ..         
T Consensus       153 ~~qq~~q~~g~~aa~q~~~~~qq~q~~~~~~~~~~~~~~~~~~~~~Qtdga~d~~~~~~~~~~~~~~~~~~~~~d~~L~~  232 (375)
T PF03153_consen  153 AAQQLQQPYGQPAAQQISQQQQQQQPQQQQQQQQQQQQPGQQVQQQQTDGAGDSESNSQPRRLEAAVPLQRNEIDQVLRS  232 (375)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccCCccccccccccccccccccccCCCccCCCcccCCCCcccchhccccccccccccccccccccc
Confidence            999999999999999999           5666666766665 3588999999852    11111111 00         


Q ss_pred             -----------CCccccccccchhhhh--hhhcccccccCCCCCCCCCCCCcCCCCcccccCCcccccccccCCCCCCCc
Q 017931          211 -----------PGRQDSVTTANREIFA--NLASSSVKIPQLDGPIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDI  277 (363)
Q Consensus       211 -----------~~~~~~~~~~~~~~~~--~~~~~~~~IPQlDGp~pdpydd~~~tpniy~yqGv~~Edyn~~~~~a~~e~  277 (363)
                                 ...+............  ...+...+|+|+||+.++..++.+.      +..+.+||+.+.        
T Consensus       233 ~i~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Q~DG~~d~~~~e~~~------~~~~~d~d~~~~--------  298 (375)
T PF03153_consen  233 QIENRAMQLEGGGLMSPLSQASKASKQNKSSNSESSRIPQLDGAGDDSDDEEDD------DDDDDDEDDEDK--------  298 (375)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccchhhccchhhcccccccccccccccccccccccCCCCCccccccc------cccccccccccc--------
Confidence                       0000000000000000  0111124699999999886655433      344566666100        


Q ss_pred             ccCCCcccccCCcCCCCCCCCCCCCCCCCCc---ccccccCCCCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeee
Q 017931          278 QASTPAVVTQNDAAEDDDDEPLNENDDDELD---DVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILF  354 (363)
Q Consensus       278 ~ast~~~~~~~~~~de~eEdpLNSdDDdd~d---D~Dd~Ed~~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF  354 (363)
                                  +.++++++.+|||+|+++|   |+|.+++++++||||||||||+|+||||||+|||||||||||||||
T Consensus       299 ------------~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~c~~~kv~r~k~~wk~~lk~g~~~~~~~d~~f  366 (375)
T PF03153_consen  299 ------------DKDEDDEDAINSDLDDSDDDVSDEDDEDDFDTDNVVLCQYDKVTRVKNKWKCTLKDGIMHINGKDYVF  366 (375)
T ss_dssp             ---------------------------------B-------STTS-EEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEE
T ss_pred             ------------cccccccccccCCcCCccccccccccccccCcCCEEEEEeeccccccceeEEEeeeeEEEECCeEEEE
Confidence                        1112234444444433222   3344457799999999999999999999999999999999999999


Q ss_pred             ecccccccC
Q 017931          355 NKATGEFDF  363 (363)
Q Consensus       355 ~KatGEfEw  363 (363)
                      +||+|||||
T Consensus       367 ~~~~ge~~w  375 (375)
T PF03153_consen  367 QKATGEFEW  375 (375)
T ss_dssp             EEEEEEEE-
T ss_pred             eeeeeeecC
Confidence            999999999

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=99.88  E-value=2.8e-23  Score=195.06  Aligned_cols=47  Identities=45%  Similarity=0.920  Sum_probs=45.5

Q ss_pred             CCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       317 ~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      ...|+|||+||||+|+|+||||+|||||+.|||+||+|+||+|||||
T Consensus       246 ~~~n~mlCLYdKVn~~K~kWKCtfkdGvV~In~~Dy~F~kAqgE~EW  292 (293)
T COG5149         246 GSTNCMLCLYDKVNMSKGKWKCTFKDGVVSINNIDYVFNKAQGELEW  292 (293)
T ss_pred             CCceEEEEEeeecccccceeeEEeecceEEecCceeEEeeccceEee
Confidence            45699999999999999999999999999999999999999999999

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	363
1rm1_C	286	Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex L		2e-09
1ytf_C	79	Yeast TfiiaTBPDNA COMPLEX Length = 79		1e-07
1nvp_C	76	Human TfiiaTBPDNA COMPLEX Length = 76		2e-07

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 34/45 (75%)
Query: 319 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F KA  E ++
Sbjct: 241 ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW 285

>pdb|1YTF|C Chain C, Yeast TfiiaTBPDNA COMPLEX Length = 79

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/45 (53%), Positives = 34/45 (75%)
Query: 319 QHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F KA  E ++
Sbjct: 34  ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW 78

>pdb|1NVP|C Chain C, Human TfiiaTBPDNA COMPLEX Length = 76

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 21/47 (44%), Positives = 39/47 (82%)
Query: 317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct: 30  DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	363
1nh2_C	79	Transcription initiation factor IIA large chain; t	1e-26
1nvp_C	76	Transcription initiation factor IIA beta chain; tr	4e-25
1rm1_C	286	Transcription initiation factor IIA large chain; y	2e-17

>1nh2_C Transcription initiation factor IIA large chain; transcription/DNA; HET: 5IU; 1.90A {Saccharomyces cerevisiae} SCOP: b.56.1.1 PDB: 1ytf_C* Length = 79

 Score =  100 bits (250), Expect = 1e-26
 Identities = 31/75 (41%), Positives = 47/75 (62%), Gaps = 1/75 (1%)

Query: 289 DAAEDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHIN 348
               D+    L+++DDD L   +  E+   ++L+L  +DKVTRTK+RWKC+LKDG++ IN
Sbjct: 5   LLDTDEVGSELDDSDDDYLIS-EGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTIN 63

Query: 349 NKDILFNKATGEFDF 363
             D  F KA  E ++
Sbjct: 64  RNDYTFQKAQVEAEW 78

>1nvp_C Transcription initiation factor IIA beta chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: b.56.1.1 Length = 76

 Score = 95.8 bits (238), Expect = 4e-25
 Identities = 28/72 (38%), Positives = 50/72 (69%), Gaps = 2/72 (2%)

Query: 292 EDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKD 351
              ++EPLN  DD   ++    E  +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D
Sbjct: 7   GQVEEEPLNSEDDVSDEEGQ--ELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRD 64

Query: 352 ILFNKATGEFDF 363
            +F+KA G+ ++
Sbjct: 65  YIFSKAIGDAEW 76

>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 = 80.7 bits (197), Expect = 2e-17
 Identities = 42/243 (17%), Positives = 79/243 (32%), Gaps = 9/243 (3%)

Query: 121 SYMPPPPSPWMNPRPPLSVDVNVAYVEGRDEADRGTSHQPLTQDFFTMSAGKRKREDFPA 180
           +               +  D+N         +      +  T +   +        + P 
Sbjct: 52  TTFSWDNQFNEGNINGVQNDLNFNLATPGVNSSEFNIKEENTGNEGLILPNINSNNNIP- 110

Query: 181 QYHNGGYNIPQQDGAGDAMSEIFELEVSEFPGRQDSVTTANREIFANLASSSVKIPQLDG 240
             H+G  NI          S       +      D  +    E+   +  +         
Sbjct: 111 --HSGETNINTNTVEATNNSGATLNTNTSGNTNADVTSQPKIEVKPEIELTINNANITTV 168

Query: 241 PIPDPYDDVLSTPNIYNYQGVVNEDYNIVNTPAPNDIQASTPAVVTQNDAAEDDDDEPLN 300
              D   +               ++   +        +    A++  ++   + DD    
Sbjct: 169 ENIDDESEKKDDEEKEEDVEKTRKEKEQIEQVKLQAKKEKRSALLDTDEVGSELDD---- 224

Query: 301 ENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGE 360
              DD+    +  E+   ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F KA  E
Sbjct: 225 --SDDDYLISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVE 282

Query: 361 FDF 363
            ++
Sbjct: 283 AEW 285

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	363
1nvp_C	76	Transcription initiation factor IIA beta chain; tr	100.0
1nh2_C	79	Transcription initiation factor IIA large chain; t	100.0
1rm1_C	286	Transcription initiation factor IIA large chain; y	99.97

>1nvp_C Transcription initiation factor IIA beta chain; transcription regulation, DNA, complex, transcription/DNA complex; 2.10A {Homo sapiens} SCOP: b.56.1.1

Probab=100.00  E-value=2.5e-36  Score=238.85  Aligned_cols=70  Identities=40%  Similarity=0.773  Sum_probs=46.8

Q ss_pred             CCCCCCCCCCCCCCCCcccccccCCCCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          292 EDDDDEPLNENDDDELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       292 de~eEdpLNSdDDdd~dD~Dd~Ed~~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      ++++||+|||+||+++++.  .++++++||||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus         7 ~~~~ed~lnsd~Dd~dd~~--~~~~~~~n~vlC~ydKV~R~KnkWKc~LKdGim~ingkdy~F~ka~GE~eW   76 (76)
T 1nvp_C            7 GQVEEEPLNSEDDVSDEEG--QELFDTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW   76 (76)
T ss_dssp             -------------------------CCCCEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEEEEC
T ss_pred             ccccccccCCcCCCccccc--ccccCCCcEEEEEEEEEeccCceEEEEEeccEEEECCEEEEEeccceeecC
Confidence            4578999999998765544  357799999999999999999999999999999999999999999999999

>1nh2_C Transcription initiation factor IIA large chain; transcription/DNA; HET: 5IU; 1.90A {Saccharomyces cerevisiae} SCOP: b.56.1.1 PDB: 1ytf_C*

Probab=100.00  E-value=1.3e-34  Score=230.55  Aligned_cols=71  Identities=42%  Similarity=0.670  Sum_probs=45.8

Q ss_pred             CCCCCCCCCCCCCCCccc---ccccCCCCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          293 DDDDEPLNENDDDELDDV---DQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       293 e~eEdpLNSdDDdd~dD~---Dd~Ed~~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      +.++|+||||+|++++|.   +++++.++.|+||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus         5 ~~d~d~insdlDd~dd~~~~~~~~~d~~~~n~vlC~ydKV~R~KnKWKc~LKdGi~~ingkDy~F~ka~GE~eW   78 (79)
T 1nh2_C            5 LLDTDEVGSELDDSDDDYLISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW   78 (79)
T ss_dssp             ----------------CCBC---------CCEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEEEEC
T ss_pred             ccccccccCccCCccccccccccccccccCcEEEEEEEEEeeecceEEEEEeeeEEEECCEEEEEecccEEEEE
Confidence            357889999987665554   33345689999999999999999999999999999999999999999999999

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

Probab=99.97  E-value=1.5e-31  Score=251.53  Aligned_cols=70  Identities=43%  Similarity=0.698  Sum_probs=49.3

Q ss_pred             CCCCCCCCCCCCCCccc---ccccCCCCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          294 DDDEPLNENDDDELDDV---DQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       294 ~eEdpLNSdDDdd~dD~---Dd~Ed~~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      .++|++|||+||+++|.   +++++..+.|+||||||||+|+||||||+|||||||||||||||+||+|||||
T Consensus       213 ~d~d~insdlDd~dd~~~~~~~~~~~~~~n~vlc~ydKV~R~knkWKc~lKdGi~~ingkdy~F~ka~GE~ew  285 (286)
T 1rm1_C          213 LDTDEVGSELDDSDDDYLISEGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW  285 (286)
T ss_dssp             ---------------CCBCCC---CSTTSCEEEEEEEEEEEETTEEEEEEEEEEEECSSCEEEEEEEEEEEEC
T ss_pred             cccccccCccCCcccccccccccccccccceEEEEEeeeeecccceeEEeeeeeEEECCceeeeeeccEEEee
Confidence            47788999986665543   34456689999999999999999999999999999999999999999999999

---

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	363
d1nvpc_	47	b.56.1.1 (C:) Large chain TOA1, C-terminal domain	1e-27
d1nh2c_	59	b.56.1.1 (C:) Large chain TOA1, C-terminal domain	4e-27

>d1nvpc_ b.56.1.1 (C:) Large chain TOA1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 47

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

 Score =  100 bits (252), Expect = 1e-27
 Identities = 21/47 (44%), Positives = 39/47 (82%)

Query: 317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           +T+++V+ Q+DK+ R+K++WK  LKDGIM++N +D +F+KA G+ ++
Sbjct: 1   DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW 47

>d1nh2c_ b.56.1.1 (C:) Large chain TOA1, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 59

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

 Score = 99.4 bits (248), Expect = 4e-27
 Identities = 27/59 (45%), Positives = 39/59 (66%), Gaps = 1/59 (1%)

Query: 305 DELDDVDQGEELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF 363
           D L   +  E+   ++L+L  +DKVTRTK+RWKC+LKDG++ IN  D  F KA  E ++
Sbjct: 1   DYLIS-EGEEDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW 58

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	363
d1nvpc_	47	Large chain TOA1, C-terminal domain {Human (Homo s	99.96
d1nh2c_	59	Large chain TOA1, C-terminal domain {Baker's yeast	99.96

>d1nvpc_ b.56.1.1 (C:) Large chain TOA1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.96  E-value=3e-31  Score=192.35  Aligned_cols=47  Identities=45%  Similarity=0.943  Sum_probs=46.1

Q ss_pred             CCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          317 NTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       317 ~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      +++|+||||||||+|+||||||+||||||+||||||||+||+|||||
T Consensus         1 ~t~n~vlc~ydKV~R~KnKWKc~lKdGim~ingkdyvF~ka~gE~eW   47 (47)
T d1nvpc_           1 DTENVVVCQYDKIHRSKNKWKFHLKDGIMNLNGRDYIFSKAIGDAEW   47 (47)
T ss_dssp             CCCCEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEEEEC
T ss_pred             CcceEEEEEEEEEEeecceEEEEEEeeEEEECCcEEEEEeeeeeecC
Confidence            48999999999999999999999999999999999999999999999

>d1nh2c_ b.56.1.1 (C:) Large chain TOA1, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

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

Probab=99.96  E-value=6.1e-31  Score=198.21  Aligned_cols=50  Identities=50%  Similarity=0.864  Sum_probs=44.8

Q ss_pred             cCCCCCCEEEEEEeeeeccCCceeEEeecceeEECCeeeeeecccccccC
Q 017931          314 EELNTQHLVLAQFDKVTRTKSRWKCALKDGIMHINNKDILFNKATGEFDF  363 (363)
Q Consensus       314 Ed~~t~NvvLCqYDKV~R~KNKWKc~LKDGIm~INGKDyvF~KatGEfEw  363 (363)
                      |+..++|+||||||||+|+||||||+||||||+||||||||+||+|||||
T Consensus         9 ed~~~~n~vlc~yDKV~R~KnKWK~~LKdGim~ingkdy~F~ka~GE~eW   58 (59)
T d1nh2c_           9 EDGPDENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEW   58 (59)
T ss_dssp             -----CCEEEEEEEEEEEETTEEEEEEEEEEEEETTEEEEEEEEEEEEEC
T ss_pred             cCCCCCcEEEEEEEEEeeccceEEEEEeeeEEEECCeEEEEeeceEEEEe
Confidence            45678999999999999999999999999999999999999999999999