Citrus Sinensis ID: 031013

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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-------
Protein Sequence
MLPYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ
Secondary Structure (PSIPRED)
ccccEEHHHcccEEEEEEEEEEEEccccccHHHHHHHccccEEccccccccccHHHHHHHHHHHHHHHHHcccccccccEEEEEEEEEEEccccccHHHHHHHcccccccccccccEEEEEEccccEEEEEEcccEEEEEccccHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEEEEEEEccccccHHHHHHHccccEEcccEEEEEccHHHHHHHHHHHHHHHHHcccccccEEEEEEEEEEEEEccccEcHHHHHHHccccEEccccccccEEEEEccccEEEEEccccEEEEEEEccHHHHHHHHHHHHHHHHHHEcccc
Coil and Loop (DISEMBL)
MLPYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARnaeynpkvctgakSEQQSKLAARKYARIIQKlgfpakfkdfkiqnivgscdvkfpirleglayshgafssyepelfpgliyrmkqpKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ
Flexible Loop (DISEMBL)
MLPYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ
Low Complexity Region (SEG)
MLPYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ
Disordered region (IsUnstruct)
**PYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTG********LAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF*****
Disordered Region (DISOPRED)
*******LILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK***
Disordered Region (DISEMBL)
MLPYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVC************ARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ
Disordered Region (DISPRO)
*********LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLPYICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ
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	167	2.2.26 [Sep-21-2011]
Q8W0W4	203	TATA-binding protein 2 OS	yes	no	0.940	0.773	0.823	4e-80
Q42808	200	TATA-box-binding protein	yes	no	0.940	0.785	0.823	2e-79
P26357	200	TATA-box-binding protein	N/A	no	0.940	0.785	0.823	3e-79
P50158	200	TATA-box-binding protein	N/A	no	0.940	0.785	0.817	5e-79
P50159	200	TATA-box-binding protein	N/A	no	0.940	0.785	0.812	5e-79
P48511	200	TATA-box-binding protein	N/A	no	0.940	0.785	0.817	1e-78
Q02879	201	TATA-box-binding protein	N/A	no	0.940	0.781	0.801	2e-78
P93348	200	TATA-box-binding protein	N/A	no	0.940	0.785	0.812	9e-78
P28148	200	TATA-box-binding protein	yes	no	0.940	0.785	0.790	1e-75
P26356	233	TATA-box-binding protein	N/A	no	0.940	0.673	0.767	3e-75

>sp|Q8W0W4|TBP2_ORYSJ TATA-binding protein 2 OS=Oryza sativa subsp. japonica GN=TBP2 PE=1 SV=2

 Score =  296 bits (758), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 154/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 23  GIIPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 82

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 83  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 142

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRKVQ
Sbjct: 143 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKVQ 202

Query: 167 Q 167
           Q
Sbjct: 203 Q 203

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q42808|TBP_SOYBN TATA-box-binding protein OS=Glycine max GN=TBP1 PE=2 SV=1

 Score =  293 bits (751), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKTIALQARNAEYNPKRFAAVIMRIRDPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRK Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKNQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Glycine max (taxid: 3847)

>sp|P26357|TBP_SOLTU TATA-box-binding protein OS=Solanum tuberosum GN=TBP PE=2 SV=1

 Score =  293 bits (751), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAY+HGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKNQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Solanum tuberosum (taxid: 4113)

>sp|P50158|TBP1_MAIZE TATA-box-binding protein 1 OS=Zea mays GN=TBP1 PE=2 SV=1

 Score =  292 bits (748), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 148/181 (81%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVR+ETYTAFENIYPVL EFRKVQ
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLAEFRKVQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Zea mays (taxid: 4577)

>sp|P50159|TBP2_MAIZE TATA-box-binding protein 2 OS=Zea mays GN=TBP2 PE=2 SV=1

 Score =  292 bits (748), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 147/181 (81%), Positives = 154/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVR+ETYTAFENIYPVL+EFRK+Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLSEFRKIQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Zea mays (taxid: 4577)

>sp|P48511|TBP_MESCR TATA-box-binding protein OS=Mesembryanthemum crystallinum PE=2 SV=1

 Score =  291 bits (746), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 148/181 (81%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVR+ETYTAFENIYPVLTEFRK Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKNQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Mesembryanthemum crystallinum (taxid: 3544)

>sp|Q02879|TBP2_WHEAT TATA-box-binding protein 2 OS=Triticum aestivum GN=TBP2 PE=2 SV=1

 Score =  290 bits (743), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 145/181 (80%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 21  GIIPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 80

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIV SCDVKFPIRLEGLAYSHGA
Sbjct: 81  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVASCDVKFPIRLEGLAYSHGA 140

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRM+QPKIVLLIFVSGKIV+TGAKVR+ETY+AFENIYPVLTEFRKVQ
Sbjct: 141 FSSYEPELFPGLIYRMRQPKIVLLIFVSGKIVLTGAKVREETYSAFENIYPVLTEFRKVQ 200

Query: 167 Q 167
           Q
Sbjct: 201 Q 201

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Triticum aestivum (taxid: 4565)

>sp|P93348|TBP_TOBAC TATA-box-binding protein OS=Nicotiana tabacum PE=2 SV=1

 Score =  288 bits (738), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 147/181 (81%), Positives = 151/181 (83%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQ SKLAARKYARIIQKLGF AKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQSSKLAARKYARIIQKLGFDAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRK Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKNQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Nicotiana tabacum (taxid: 4097)

>sp|P28148|TBP2_ARATH TATA-box-binding protein 2 OS=Arabidopsis thaliana GN=TBP2 PE=1 SV=1

 Score =  281 bits (720), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 143/181 (79%), Positives = 149/181 (82%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE  SKLAARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 80  VCTGAKSEHLSKLAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHSA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+R+ETYTAFENIYPVL EFRKVQ
Sbjct: 140 FSSYEPELFPGLIYRMKLPKIVLLIFVSGKIVITGAKMREETYTAFENIYPVLREFRKVQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Arabidopsis thaliana (taxid: 3702)

>sp|P26356|TBP1_WHEAT TATA-box-binding protein 1 OS=Triticum aestivum GN=TBP1 PE=2 SV=1

 Score =  280 bits (716), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 139/181 (76%), Positives = 148/181 (81%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNLDC+LDLK+IALQARNAEYNPK                        
Sbjct: 53  GIVPVLQNIVSTVNLDCRLDLKQIALQARNAEYNPKRFAAVIMRIRDPKTTALIFASGKM 112

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE+ SKLAARKYARI+QKLGFPA FKDFKIQNIV SCDVKFPIRLEGLAYSHGA
Sbjct: 113 VCTGAKSEEHSKLAARKYARIVQKLGFPATFKDFKIQNIVASCDVKFPIRLEGLAYSHGA 172

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLL+FVSGKIV+TGAKVRDE Y AFENIYPVLTE+RK Q
Sbjct: 173 FSSYEPELFPGLIYRMKQPKIVLLVFVSGKIVLTGAKVRDEIYAAFENIYPVLTEYRKSQ 232

Query: 167 Q 167
           Q
Sbjct: 233 Q 233

General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II.

Triticum aestivum (taxid: 4565)

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	167
255568956	201	TATA-box binding protein, putative [Rici	0.940	0.781	0.834	4e-79
218193429	190	hypothetical protein OsI_12863 [Oryza sa	0.964	0.847	0.813	6e-79
115454423	203	Os03g0657000 [Oryza sativa Japonica Grou	0.940	0.773	0.823	2e-78
222625492	207	hypothetical protein OsJ_11965 [Oryza sa	0.940	0.758	0.823	3e-78
357119735	200	PREDICTED: TATA-box-binding protein 2-li	0.940	0.785	0.817	5e-78
242084298	200	hypothetical protein SORBIDRAFT_08g02227	0.940	0.785	0.823	5e-78
242038657	200	hypothetical protein SORBIDRAFT_01g01288	0.940	0.785	0.823	6e-78
224285248	200	unknown [Picea sitchensis]	0.940	0.785	0.812	9e-78
351727953	200	TATA-box-binding protein [Glycine max] g	0.940	0.785	0.823	1e-77
357155673	202	PREDICTED: TATA-box-binding protein 2-li	0.940	0.777	0.817	1e-77

>gi|255568956|ref|XP_002525448.1| TATA-box binding protein, putative [Ricinus communis] gi|223535261|gb|EEF36938.1| TATA-box binding protein, putative [Ricinus communis]

 Score =  298 bits (764), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 151/181 (83%), Positives = 155/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK+IALQARNAEYNPK                        
Sbjct: 21  GIVPTLQNIVSTVNLDCKLDLKQIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 80

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 81  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 140

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ
Sbjct: 141 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 200

Query: 167 Q 167
           Q
Sbjct: 201 Q 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218193429|gb|EEC75856.1| hypothetical protein OsI_12863 [Oryza sativa Indica Group]

 Score =  298 bits (762), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 153/188 (81%), Positives = 156/188 (82%), Gaps = 27/188 (14%)

Query: 4   YICYLILGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK----------------- 46
           YIC L+  A    +NIVSTVNLDCKLDLK IALQARNAEYNPK                 
Sbjct: 2   YICMLVCAAK---RNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTAL 58

Query: 47  -------VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEG 99
                  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEG
Sbjct: 59  IFASGKMVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEG 118

Query: 100 LAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 159
           LAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVL
Sbjct: 119 LAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVL 178

Query: 160 TEFRKVQQ 167
           TEFRKVQQ
Sbjct: 179 TEFRKVQQ 186

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115454423|ref|NP_001050812.1| Os03g0657000 [Oryza sativa Japonica Group] gi|73919858|sp|Q8W0W4.2|TBP2_ORYSJ RecName: Full=TATA-binding protein 2; AltName: Full=TATA sequence-binding protein 2; Short=TBP-2; AltName: Full=TATA-binding factor 2; AltName: Full=TATA-box factor 2; AltName: Full=Transcription initiation factor TFIID TBP-2 subunit gi|31415973|gb|AAP50993.1| TATA-binding protein TBP2 [Oryza sativa Japonica Group] gi|108710181|gb|ABF97976.1| TATA-binding protein 2, putative, expressed [Oryza sativa Japonica Group] gi|113549283|dbj|BAF12726.1| Os03g0657000 [Oryza sativa Japonica Group] gi|215686467|dbj|BAG87728.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  296 bits (758), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 154/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 23  GIIPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 82

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 83  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 142

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRKVQ
Sbjct: 143 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKVQ 202

Query: 167 Q 167
           Q
Sbjct: 203 Q 203

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222625492|gb|EEE59624.1| hypothetical protein OsJ_11965 [Oryza sativa Japonica Group]

 Score =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 154/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 23  GIIPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 82

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 83  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 142

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRKVQ
Sbjct: 143 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKVQ 202

Query: 167 Q 167
           Q
Sbjct: 203 Q 203

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357119735|ref|XP_003561589.1| PREDICTED: TATA-box-binding protein 2-like [Brachypodium distachyon]

 Score =  295 bits (754), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 148/181 (81%), Positives = 154/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIIPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVR+ETYTAFENIYPVLTEFRKVQ
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKVQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242084298|ref|XP_002442574.1| hypothetical protein SORBIDRAFT_08g022273 [Sorghum bicolor] gi|241943267|gb|EES16412.1| hypothetical protein SORBIDRAFT_08g022273 [Sorghum bicolor]

 Score =  295 bits (754), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE QSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEHQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRKVQ
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKVQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242038657|ref|XP_002466723.1| hypothetical protein SORBIDRAFT_01g012880 [Sorghum bicolor] gi|241920577|gb|EER93721.1| hypothetical protein SORBIDRAFT_01g012880 [Sorghum bicolor]

 Score =  295 bits (754), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 154/181 (85%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVR+ETYTAFENIYPVLTEFRKVQ
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKVQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224285248|gb|ACN40350.1| unknown [Picea sitchensis]

 Score =  294 bits (752), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 147/181 (81%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIIPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPA FKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAHFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRK+Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKIQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727953|ref|NP_001238202.1| TATA-box-binding protein [Glycine max] gi|3122946|sp|Q42808.1|TBP_SOYBN RecName: Full=TATA-box-binding protein; AltName: Full=TATA sequence-binding protein; Short=TBP; AltName: Full=TATA-binding factor; AltName: Full=TATA-box factor; AltName: Full=Transcription initiation factor TFIID TBP subunit gi|1220522|gb|AAA91948.1| TATA-box binding protein [Glycine max]

 Score =  293 bits (751), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 149/181 (82%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKTIALQARNAEYNPKRFAAVIMRIRDPKTTALIFASGKM 79

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 80  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 139

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV+TGAKVRDETYTAFENIYPVLTEFRK Q
Sbjct: 140 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKNQ 199

Query: 167 Q 167
           Q
Sbjct: 200 Q 200

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357155673|ref|XP_003577198.1| PREDICTED: TATA-box-binding protein 2-like [Brachypodium distachyon]

 Score =  293 bits (751), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 148/181 (81%), Positives = 153/181 (84%), Gaps = 24/181 (13%)

Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 22  GIVPMLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 81

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA
Sbjct: 82  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 141

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRM+QPKIVLLIFVSGKIV+TGAKVR+ETYTAFENIYPVLTEFRKVQ
Sbjct: 142 FSSYEPELFPGLIYRMRQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKVQ 201

Query: 167 Q 167
           Q
Sbjct: 202 Q 202

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	167
TAIR|locus:2193904	200	TBP2 "TATA binding protein 2"	0.724	0.605	0.933	2.9e-70
TAIR|locus:2092905	200	TBP1 "TATA binding protein 1"	0.724	0.605	0.917	7.7e-70
POMBASE|SPAC29E6.08	231	tbp1 "TATA-binding protein (TB	0.706	0.510	0.847	6.1e-62
ZFIN|ZDB-GENE-030616-563	302	tbp "TATA box binding protein"	0.706	0.390	0.813	2e-61
UNIPROTKB|O13270	302	TBP "TATA-box-binding protein"	0.706	0.390	0.813	2.6e-61
UNIPROTKB|Q6JLB1	302	TBP "TATA-binding protein" [Ga	0.706	0.390	0.813	2.6e-61
UNIPROTKB|Q2HJ52	319	TBP "TATA-box-binding protein"	0.706	0.369	0.813	2.6e-61
UNIPROTKB|F1PQA5	324	TBP "Uncharacterized protein"	0.706	0.364	0.813	2.6e-61
UNIPROTKB|P20226	339	TBP "TATA-box-binding protein"	0.706	0.348	0.813	2.6e-61
UNIPROTKB|P27633	297	tbp "TATA-box-binding protein"	0.706	0.397	0.813	2.6e-61

TAIR|locus:2193904 TBP2 "TATA binding protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 578 (208.5 bits), Expect = 2.9e-70, Sum P(2) = 2.9e-70
 Identities = 113/121 (93%), Positives = 116/121 (95%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE  SKLAARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct:    80 VCTGAKSEHLSKLAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHSA 139

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
             FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+R+ETYTAFENIYPVL EFRKVQ
Sbjct:   140 FSSYEPELFPGLIYRMKLPKIVLLIFVSGKIVITGAKMREETYTAFENIYPVLREFRKVQ 199

Query:   167 Q 167
             Q
Sbjct:   200 Q 200

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

GO:0005634 "nucleus" evidence=ISM;TAS

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

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2092905 TBP1 "TATA binding protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 574 (207.1 bits), Expect = 7.7e-70, Sum P(2) = 7.7e-70
 Identities = 111/121 (91%), Positives = 116/121 (95%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE  SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct:    80 VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 139

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
             FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+Q
Sbjct:   140 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 199

Query:   167 Q 167
             Q
Sbjct:   200 Q 200

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

POMBASE|SPAC29E6.08 tbp1 "TATA-binding protein (TBP)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 509 (184.2 bits), Expect = 6.1e-62, Sum P(2) = 6.1e-62
 Identities = 100/118 (84%), Positives = 106/118 (89%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             V  G KSE  SKLA+RKYARIIQKLGF AKF DFKIQNIVGSCDVKFPIRLEGLAYSHG 
Sbjct:   113 VVLGGKSEDDSKLASRKYARIIQKLGFNAKFTDFKIQNIVGSCDVKFPIRLEGLAYSHGT 172

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +PK+VLLIFVSGKIV+TGAKVR+E Y AFE IYPVL+EFRK
Sbjct:   173 FSSYEPELFPGLIYRMVKPKVVLLIFVSGKIVLTGAKVREEIYQAFEAIYPVLSEFRK 230

GO:0000120 "RNA polymerase I transcription factor complex" evidence=ISO

GO:0000126 "transcription factor TFIIIB complex" evidence=ISO

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

GO:0000995 "core RNA polymerase III binding transcription factor activity" evidence=ISO

GO:0001169 "RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

GO:0006360 "transcription from RNA polymerase I promoter" evidence=ISO

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

GO:0006384 "transcription initiation from RNA polymerase III promoter" evidence=ISO

ZFIN|ZDB-GENE-030616-563 tbp "TATA box binding protein" [Danio rerio (taxid:7955)]

 Score = 506 (183.2 bits), Expect = 2.0e-61, Sum P(2) = 2.0e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   183 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 242

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   243 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRGEIYEAFENIYPILKGFRK 300

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA;ISS

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

GO:0006402 "mRNA catabolic process" evidence=IMP

GO:0007369 "gastrulation" evidence=IEA;IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

UNIPROTKB|O13270 TBP "TATA-box-binding protein" [Gallus gallus (taxid:9031)]

 Score = 505 (182.8 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   183 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 242

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   243 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 300

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q6JLB1 TBP "TATA-binding protein" [Gallus gallus (taxid:9031)]

 Score = 505 (182.8 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   183 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 242

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   243 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 300

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

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

GO:0001939 "female pronucleus" evidence=IEA

GO:0001940 "male pronucleus" evidence=IEA

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

GO:0005719 "nuclear euchromatin" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0006383 "transcription from RNA polymerase III promoter" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

UNIPROTKB|Q2HJ52 TBP "TATA-box-binding protein" [Bos taurus (taxid:9913)]

 Score = 505 (182.8 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   200 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 259

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   260 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 317

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|F1PQA5 TBP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 505 (182.8 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   205 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 264

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   265 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 322

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0006383 "transcription from RNA polymerase III promoter" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005719 "nuclear euchromatin" evidence=IEA

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

GO:0001940 "male pronucleus" evidence=IEA

GO:0001939 "female pronucleus" evidence=IEA

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|P20226 TBP "TATA-box-binding protein" [Homo sapiens (taxid:9606)]

 Score = 505 (182.8 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   220 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 279

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   280 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 337

GO:0008219 "cell death" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

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

GO:0001939 "female pronucleus" evidence=IEA

GO:0001940 "male pronucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005669 "transcription factor TFIID complex" evidence=IDA

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

GO:0008134 "transcription factor binding" evidence=IPI

GO:0044212 "transcription regulatory region DNA binding" evidence=IDA

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

GO:0006383 "transcription from RNA polymerase III promoter" evidence=IDA;TAS

GO:0005654 "nucleoplasm" 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:0005672 "transcription factor TFIIA complex" evidence=IDA

GO:0005719 "nuclear euchromatin" evidence=IDA

GO:0070491 "repressing transcription factor binding" evidence=IPI

UNIPROTKB|P27633 tbp "TATA-box-binding protein" [Xenopus laevis (taxid:8355)]

 Score = 505 (182.8 bits), Expect = 2.6e-61, Sum P(2) = 2.6e-61
 Identities = 96/118 (81%), Positives = 107/118 (90%)

Query:    47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct:   178 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 237

Query:   107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
             FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct:   238 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 295

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005669 "transcription factor TFIID complex" evidence=NAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IMP;NAS

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

GO:0009790 "embryo development" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P13393	TBP_YEAST	No assigned EC number	0.6927	0.9281	0.6458	yes	no
P28148	TBP2_ARATH	No assigned EC number	0.7900	0.9401	0.785	yes	no
P50159	TBP2_MAIZE	No assigned EC number	0.8121	0.9401	0.785	N/A	no
P50158	TBP1_MAIZE	No assigned EC number	0.8176	0.9401	0.785	N/A	no
O43133	TBP_CANAL	No assigned EC number	0.7045	0.9101	0.6386	N/A	no
P26356	TBP1_WHEAT	No assigned EC number	0.7679	0.9401	0.6738	N/A	no
P26357	TBP_SOLTU	No assigned EC number	0.8232	0.9401	0.785	N/A	no
P26354	TBP_ACACA	No assigned EC number	0.7094	0.9281	0.6007	N/A	no
P26355	TBP_DICDI	No assigned EC number	0.6444	0.9341	0.7609	yes	no
P46272	TBP_ACECL	No assigned EC number	0.6741	0.9221	0.8062	N/A	no
Q42808	TBP_SOYBN	No assigned EC number	0.8232	0.9401	0.785	yes	no
P93348	TBP_TOBAC	No assigned EC number	0.8121	0.9401	0.785	N/A	no
Q12731	TBP_EMENI	No assigned EC number	0.7039	0.9281	0.5783	yes	no
Q8W0W4	TBP2_ORYSJ	No assigned EC number	0.8232	0.9401	0.7733	yes	no
P17871	TBP_SCHPO	No assigned EC number	0.7055	0.9341	0.6753	yes	no
P48511	TBP_MESCR	No assigned EC number	0.8176	0.9401	0.785	N/A	no
Q02879	TBP2_WHEAT	No assigned EC number	0.8011	0.9401	0.7810	N/A	no

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:
	BRADI1G13220.1	annotation not avaliable (200 aa)
		(Brachypodium distachyon)
Predicted Functional Partners:
	BRADI4G36290.1	annotation not avaliable (312 aa)			•		•	•	•		0.919
	BRADI2G17730.1	annotation not avaliable (338 aa)			•		•		•		0.655
	BRADI2G39380.1	annotation not avaliable (190 aa)					•	•	•		0.606
	BRADI1G30900.1	annotation not avaliable (678 aa)					•	•	•		0.494
	BRADI3G52730.1	annotation not avaliable (288 aa)							•		0.468
	BRADI1G54820.1	annotation not avaliable (203 aa)					•	•	•		0.465
	BRADI4G27220.1	annotation not avaliable (545 aa)					•	•	•		0.449
	BRADI3G16660.1	annotation not avaliable (1862 aa)					•	•	•		0.435
	BRADI4G08350.1	annotation not avaliable (330 aa)			•		•	•	•		0.421
	BRADI3G05850.1	annotation not avaliable (1244 aa)			•			•			0.412

---

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	167
PLN00062	179	PLN00062, PLN00062, TATA-box-binding protein; Prov	1e-107
cd04516	174	cd04516, TBP_eukaryotes, eukaryotic TATA box bindi	7e-99
cd00652	174	cd00652, TBP_TLF, TATA box binding protein (TBP):	1e-85
COG2101	185	COG2101, SPT15, TATA-box binding protein (TBP), co	1e-63
cd04517	174	cd04517, TLF, TBP-like factors (TLF; also called T	4e-51
pfam00352	86	pfam00352, TBP, Transcription factor TFIID (or TAT	6e-42
PRK00394	179	PRK00394, PRK00394, transcription factor; Reviewed	1e-41
cd04518	174	cd04518, TBP_archaea, archaeal TATA box binding pr	2e-38
PRK00394	179	PRK00394, PRK00394, transcription factor; Reviewed	7e-20
pfam00352	86	pfam00352, TBP, Transcription factor TFIID (or TAT	8e-19
COG2101	185	COG2101, SPT15, TATA-box binding protein (TBP), co	2e-17
cd04518	174	cd04518, TBP_archaea, archaeal TATA box binding pr	1e-15
cd00652	174	cd00652, TBP_TLF, TATA box binding protein (TBP):	6e-15
cd04518	174	cd04518, TBP_archaea, archaeal TATA box binding pr	1e-06
PRK00394	179	PRK00394, PRK00394, transcription factor; Reviewed	9e-06
COG2101	185	COG2101, SPT15, TATA-box binding protein (TBP), co	5e-04

>gnl|CDD|177693 PLN00062, PLN00062, TATA-box-binding protein; Provisional

 Score =  302 bits (776), Expect = e-107
 Identities = 145/179 (81%), Positives = 150/179 (83%), Gaps = 24/179 (13%)

Query: 13  VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VC 48
           V +++NIVSTVNLDCKLDLKKIALQARNAEYNPK                        VC
Sbjct: 1   VPTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVC 60

Query: 49  TGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
           TGAKSE  SKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAY+HGAFS
Sbjct: 61  TGAKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFS 120

Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ 167
           SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR+E YTAFENIYPVLTEFRK QQ
Sbjct: 121 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYPVLTEFRKRQQ 179

Length = 179

>gnl|CDD|239952 cd04516, TBP_eukaryotes, eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

 Score =  281 bits (722), Expect = 7e-99
 Identities = 125/171 (73%), Positives = 136/171 (79%), Gaps = 24/171 (14%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV+TVNL CKLDLKKIAL+ARNAEYNPK                        VCTGA
Sbjct: 4   IQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGA 63

Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYE 111
           KSE  SKLAARKYARIIQKLGFPAKF DFKIQNIVGSCDVKFPIRLEGLA++H  FSSYE
Sbjct: 64  KSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYE 123

Query: 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
           PELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFENIYP+L +F
Sbjct: 124 PELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIYQAFENIYPILLQF 174

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. Length = 174

>gnl|CDD|238352 cd00652, TBP_TLF, TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

 Score =  248 bits (635), Expect = 1e-85
 Identities = 108/171 (63%), Positives = 125/171 (73%), Gaps = 25/171 (14%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV+TVNL C+LDL+KIAL ARNAEYNPK                        V TGA
Sbjct: 4   IQNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGA 63

Query: 52  KSEQQSKLAARKYARIIQKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSY 110
           KSE+ +KLAARKYARI+QKLGFP  KF +FK+QNIV SCD+ FPIRLE LA  H   +SY
Sbjct: 64  KSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASY 123

Query: 111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 161
           EPELFPGLIYRM +PK+VLLIFVSGKIVITGAK R++ Y A E IYP+L E
Sbjct: 124 EPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILKE 174

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP. Length = 174

>gnl|CDD|225012 COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

 Score =  192 bits (491), Expect = 1e-63
 Identities = 66/174 (37%), Positives = 95/174 (54%), Gaps = 26/174 (14%)

Query: 18  NIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKS 53
           NIV++V+L  +LDL+++AL    AEYNP+                        VCTGAKS
Sbjct: 12  NIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKS 71

Query: 54  EQQSKLAARKYARIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGAF-SSYE 111
            +    A +K A+ ++  G    F+ + K+QNIV S D+   + L  +A   G     YE
Sbjct: 72  VEDVHRAVKKLAKKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYE 131

Query: 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           PE FPGL+YR+ +P++VLL+F SGK+VITGAK  ++   A E I   L E   +
Sbjct: 132 PEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEELGLL 185

Length = 185

>gnl|CDD|239953 cd04517, TLF, TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans

 Score =  160 bits (408), Expect = 4e-51
 Identities = 66/170 (38%), Positives = 103/170 (60%), Gaps = 24/170 (14%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPKV-----------------------CTGAK 52
           + N+V   +L C +DL+K+AL  RN EYNP+                         TGA 
Sbjct: 5   IVNVVCQFSLRCHIDLRKLALAGRNVEYNPRYPKVTMRLREPRATASVWSSGKITITGAT 64

Query: 53  SEQQSKLAARKYARIIQKLGFP-AKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYE 111
           SE+++K AAR+ AR++QKLGF   +F +F++ N++ +C + FPIRL+ LA  + + +SYE
Sbjct: 65  SEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYE 124

Query: 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 161
           PEL PG++YR+  P+  L IF +G + +TGA+  ++   A E IYP++ E
Sbjct: 125 PELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIVFE 174

TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters. Length = 174

>gnl|CDD|201174 pfam00352, TBP, Transcription factor TFIID (or TATA-binding protein, TBP)

 Score =  134 bits (341), Expect = 6e-42
 Identities = 44/87 (50%), Positives = 56/87 (64%), Gaps = 1/87 (1%)

Query: 77  FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGK 136
           F D KIQNIV S D+ FPI LE +A      + YEPE FPGL+YR+++PK   LIF SGK
Sbjct: 1   FPDIKIQNIVASADLGFPIDLEKIALKLR-NAEYEPEQFPGLVYRLREPKATALIFSSGK 59

Query: 137 IVITGAKVRDETYTAFENIYPVLTEFR 163
           +VITGAK  ++   A   I P+L +  
Sbjct: 60  VVITGAKSEEDAKKAVRKIAPILKKLG 86

Length = 86

>gnl|CDD|234746 PRK00394, PRK00394, transcription factor; Reviewed

 Score =  136 bits (346), Expect = 1e-41
 Identities = 64/171 (37%), Positives = 92/171 (53%), Gaps = 26/171 (15%)

Query: 18  NIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKS 53
           NIV++ +L  +LDL+K+A    NAEYNP+                        VCTGAKS
Sbjct: 5   NIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKS 64

Query: 54  EQQSKLAARKYARIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSS-YE 111
            +    A +   + +++LG     + + K+QNIV S D+   + L  +A   G  +  YE
Sbjct: 65  VEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYE 124

Query: 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
           PE FPGL+YR+  PK+V+L+F SGK+VITGAK  ++   A E I   L E 
Sbjct: 125 PEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKILEKLEEL 175

Length = 179

>gnl|CDD|239954 cd04518, TBP_archaea, archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription

 Score =  128 bits (324), Expect = 2e-38
 Identities = 64/171 (37%), Positives = 95/171 (55%), Gaps = 26/171 (15%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++V+L  +LDL+K+A +  NAEYNP                         VCTGA
Sbjct: 4   IENIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGA 63

Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSY 110
           KS +    A ++  + ++  G     K + K+QNIV S D+   + L+ +A      + Y
Sbjct: 64  KSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLPN-AEY 122

Query: 111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 161
           EPE FPGL+YR+ +PK+VLL+F SGK+VITGAK  ++   A E +   L E
Sbjct: 123 EPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLSRLKE 173

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. Length = 174

>gnl|CDD|234746 PRK00394, PRK00394, transcription factor; Reviewed

 Score = 81.0 bits (201), Expect = 7e-20
 Identities = 35/75 (46%), Positives = 48/75 (64%), Gaps = 1/75 (1%)

Query: 81  KIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVIT 140
           KI+NIV S D+   + LE +A      + Y PE FPGL+YR++ PKI  LIF SGK+V T
Sbjct: 2   KIENIVASTDLGQELDLEKVAEDLPN-AEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCT 60

Query: 141 GAKVRDETYTAFENI 155
           GAK  ++ + A + I
Sbjct: 61  GAKSVEDLHEAVKII 75

Length = 179

>gnl|CDD|201174 pfam00352, TBP, Transcription factor TFIID (or TATA-binding protein, TBP)

 Score = 75.6 bits (187), Expect = 8e-19
 Identities = 32/81 (39%), Positives = 45/81 (55%), Gaps = 24/81 (29%)

Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
          ++NIV++ +L   +DL+KIAL+ RNAEY P+                        V TGA
Sbjct: 6  IQNIVASADLGFPIDLEKIALKLRNAEYEPEQFPGLVYRLREPKATALIFSSGKVVITGA 65

Query: 52 KSEQQSKLAARKYARIIQKLG 72
          KSE+ +K A RK A I++KLG
Sbjct: 66 KSEEDAKKAVRKIAPILKKLG 86

Length = 86

>gnl|CDD|225012 COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

 Score = 74.7 bits (184), Expect = 2e-17
 Identities = 32/75 (42%), Positives = 47/75 (62%), Gaps = 1/75 (1%)

Query: 81  KIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVIT 140
            I+NIV S D+   + LE +A      + Y PE FPGL+YR+++PK   LIF SGK+V T
Sbjct: 9   TIENIVASVDLGQELDLEEVA-LDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCT 67

Query: 141 GAKVRDETYTAFENI 155
           GAK  ++ + A + +
Sbjct: 68  GAKSVEDVHRAVKKL 82

Length = 185

>gnl|CDD|239954 cd04518, TBP_archaea, archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription

 Score = 70.0 bits (172), Expect = 1e-15
 Identities = 34/75 (45%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 81  KIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVIT 140
           KI+NIV S D+   + LE +A +    + Y P+ FPGL+YR++ PKI  LIF SGK+V T
Sbjct: 3   KIENIVASVDLGQELDLEKVA-AELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCT 61

Query: 141 GAKVRDETYTAFENI 155
           GAK  ++ + A + I
Sbjct: 62  GAKSVEDLHRAVKEI 76

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. Length = 174

>gnl|CDD|238352 cd00652, TBP_TLF, TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

 Score = 68.0 bits (167), Expect = 6e-15
 Identities = 29/65 (44%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
             KIQNIV + ++   + L  +A      + Y P+ FPG+I R+++PK   LIF SGK+V
Sbjct: 1   SPKIQNIVATVNLGCELDLRKIA-LAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMV 59

Query: 139 ITGAK 143
           ITGAK
Sbjct: 60  ITGAK 64

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP. Length = 174

>gnl|CDD|239954 cd04518, TBP_archaea, archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 24/80 (30%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           V+NIV++ +L  +++L  IA+   NAEY P+                        V TGA
Sbjct: 95  VQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGA 154

Query: 52  KSEQQSKLAARKYARIIQKL 71
           KSE+ +K A  K    +++L
Sbjct: 155 KSEEDAKRAVEKLLSRLKEL 174

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. Length = 174

>gnl|CDD|234746 PRK00394, PRK00394, transcription factor; Reviewed

 Score = 43.3 bits (103), Expect = 9e-06
 Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 26/83 (31%)

Query: 16  VKNIVSTVNLDCKLDLKKIA--LQARNAEYNPK------------------------VCT 49
           V+NIV++ +L  +L+L  IA  L   N EY P+                        V T
Sbjct: 94  VQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVIT 153

Query: 50  GAKSEQQSKLAARKYARIIQKLG 72
           GAKSE+ ++ A  K    +++LG
Sbjct: 154 GAKSEEDAEKAVEKILEKLEELG 176

Length = 179

>gnl|CDD|225012 COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 26/83 (31%)

Query: 16  VKNIVSTVNLDCKLDLKKIA--LQARNAEYNPK------------------------VCT 49
           V+NIV++ +L  +L+L  IA  L   N EY P+                        V T
Sbjct: 101 VQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVIT 160

Query: 50  GAKSEQQSKLAARKYARIIQKLG 72
           GAKSE+ ++ A  K    +++LG
Sbjct: 161 GAKSEEDAEQAVEKIQSRLEELG 183

Length = 185

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	167
KOG3302	200	consensus TATA-box binding protein (TBP), componen	100.0
PLN00062	179	TATA-box-binding protein; Provisional	100.0
cd04516	174	TBP_eukaryotes eukaryotic TATA box binding protein	100.0
COG2101	185	SPT15 TATA-box binding protein (TBP), component of	100.0
cd04518	174	TBP_archaea archaeal TATA box binding protein (TBP	100.0
PRK00394	179	transcription factor; Reviewed	100.0
cd00652	174	TBP_TLF TATA box binding protein (TBP): Present in	100.0
cd04517	174	TLF TBP-like factors (TLF; also called TLP, TRF, T	100.0
PF00352	86	TBP: Transcription factor TFIID (or TATA-binding p	100.0
cd04516	174	TBP_eukaryotes eukaryotic TATA box binding protein	99.96
PLN00062	179	TATA-box-binding protein; Provisional	99.96
cd04518	174	TBP_archaea archaeal TATA box binding protein (TBP	99.95
PRK00394	179	transcription factor; Reviewed	99.95
COG2101	185	SPT15 TATA-box binding protein (TBP), component of	99.95
cd00652	174	TBP_TLF TATA box binding protein (TBP): Present in	99.95
cd04517	174	TLF TBP-like factors (TLF; also called TLP, TRF, T	99.94
KOG3302	200	consensus TATA-box binding protein (TBP), componen	99.86
PF00352	86	TBP: Transcription factor TFIID (or TATA-binding p	99.73
PF11858	81	DUF3378: Domain of unknown function (DUF3378); Int	96.85
COG4871	193	Uncharacterized protein conserved in archaea [Func	95.5
COG1039	297	RnhC Ribonuclease HIII [DNA replication, recombina	94.9
PRK00996	304	ribonuclease HIII; Provisional	94.26
TIGR00716	284	rnhC ribonuclease HIII. Two types of ribonuclease	94.03
PRK12475	338	thiamine/molybdopterin biosynthesis MoeB-like prot	84.52

>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

Probab=100.00  E-value=7.1e-59  Score=372.95  Aligned_cols=158  Identities=75%  Similarity=1.204  Sum_probs=154.6

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      .++.|.++||||+++++|+|||++||+.++|+||||+                        +||||+|+++||.|++|++
T Consensus        19 ~~i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~a   98 (200)
T KOG3302|consen   19 SGLDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYA   98 (200)
T ss_pred             cccceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999998                        8999999999999999999


Q ss_pred             HHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013           66 RIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR  145 (167)
Q Consensus        66 ~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~  145 (167)
                      |+||+|||+++|.+|+|||||||||++|+|+|++++..|+.+++||||+||||+|||.+|+++++||+||||++|||++.
T Consensus        99 RilqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~  178 (200)
T KOG3302|consen   99 RILQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVR  178 (200)
T ss_pred             HHHHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhhhcC
Q 031013          146 DETYTAFENIYPVLTEFRKVQQ  167 (167)
Q Consensus       146 e~~~~a~~~i~~~L~~~r~~~~  167 (167)
                      +|+.+|+++|||+|.+|||+.+
T Consensus       179 ~~i~~Ai~~IyPil~~frk~~~  200 (200)
T KOG3302|consen  179 EETYEAIENIYPILLEFRKKLL  200 (200)
T ss_pred             HHHHHHHHHHhHHHHHhhhccC
Confidence            9999999999999999999753

>PLN00062 TATA-box-binding protein; Provisional

Probab=100.00  E-value=4.7e-58  Score=367.83  Aligned_cols=155  Identities=94%  Similarity=1.393  Sum_probs=151.2

Q ss_pred             eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013           13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII   68 (167)
Q Consensus        13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l   68 (167)
                      .|+|+|||||++++|+|||++||..++|++|||+                        +||||+|+++|+.|+++++++|
T Consensus         1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L   80 (179)
T PLN00062          1 VPTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII   80 (179)
T ss_pred             CcEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999999998                        8999999999999999999999


Q ss_pred             HhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013           69 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET  148 (167)
Q Consensus        69 ~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~  148 (167)
                      +++|+++++.+|+|+|||||+|++++|||+.||..+.++++||||+||||+||+.+|+++++||+||||+|||+||++|+
T Consensus        81 ~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~  160 (179)
T PLN00062         81 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEI  160 (179)
T ss_pred             HHcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHH
Confidence            99999999999999999999999999999999987778999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhhcC
Q 031013          149 YTAFENIYPVLTEFRKVQQ  167 (167)
Q Consensus       149 ~~a~~~i~~~L~~~r~~~~  167 (167)
                      ++|++.|+|+|.+||+.+|
T Consensus       161 ~~ai~~i~p~L~~~~~~~~  179 (179)
T PLN00062        161 YTAFENIYPVLTEFRKRQQ  179 (179)
T ss_pred             HHHHHHHHHHHHHhccCCC
Confidence            9999999999999998865

>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

Probab=100.00  E-value=4.9e-57  Score=360.55  Aligned_cols=150  Identities=84%  Similarity=1.302  Sum_probs=146.5

Q ss_pred             eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013           13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII   68 (167)
Q Consensus        13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l   68 (167)
                      .|+|+|||||++++|+|||++||..++|++|||+                        +||||+|+|+|+.|+++++++|
T Consensus         1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L   80 (174)
T cd04516           1 VPKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII   80 (174)
T ss_pred             CCEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999999998                        8999999999999999999999


Q ss_pred             HhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013           69 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET  148 (167)
Q Consensus        69 ~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~  148 (167)
                      +++|+++++.+|+|+|||||+|++++|||++||..+.++++||||+||||+||+.+|+++++||+||||+|||+||++|+
T Consensus        81 ~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~  160 (174)
T cd04516          81 QKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEI  160 (174)
T ss_pred             HHcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHH
Confidence            99999999999999999999999999999999988777999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 031013          149 YTAFENIYPVLTEF  162 (167)
Q Consensus       149 ~~a~~~i~~~L~~~  162 (167)
                      ++|+++|+|+|.+|
T Consensus       161 ~~a~~~i~p~L~~~  174 (174)
T cd04516         161 YQAFENIYPILLQF  174 (174)
T ss_pred             HHHHHHHHHHHhhC
Confidence            99999999999886

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.

>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

Probab=100.00  E-value=5.4e-56  Score=351.51  Aligned_cols=155  Identities=43%  Similarity=0.705  Sum_probs=148.5

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      .++.++|+|||||++|+++|||++++..++|+||||+                        +||||||+++++.|.++++
T Consensus         4 ~~~~i~IeNIVAS~~L~~elDL~~~~~~l~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~   83 (185)
T COG2101           4 SEPTITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLA   83 (185)
T ss_pred             CCCccEEEEEEEEechhhhccHHHHHhhCCCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999                        9999999999999999999


Q ss_pred             HHHHhcCCCCccc-ceEEEEEEEEEecCCccchHhHHHHcC-CCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccC
Q 031013           66 RIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHG-AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAK  143 (167)
Q Consensus        66 ~~l~~lg~~~~~~-~~~I~NIvas~~l~~~I~L~~la~~~~-~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGak  143 (167)
                      ++|+++|+++.+. .++|||||||+|+++++||+.+|..++ ++++|||||||||+||+.+|++++|||+|||+||||||
T Consensus        84 ~~L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK  163 (185)
T COG2101          84 KKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAK  163 (185)
T ss_pred             HHHHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCC
Confidence            9999999998764 899999999999999999999999886 36999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHhhhh
Q 031013          144 VRDETYTAFENIYPVLTEFRK  164 (167)
Q Consensus       144 s~e~~~~a~~~i~~~L~~~r~  164 (167)
                      +++|+++|++++++.|.++..
T Consensus       164 ~~ed~~~Av~~i~~~L~elgl  184 (185)
T COG2101         164 SEEDAEQAVEKIQSRLEELGL  184 (185)
T ss_pred             CHHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999998753

>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription

Probab=100.00  E-value=9.4e-55  Score=347.39  Aligned_cols=149  Identities=42%  Similarity=0.697  Sum_probs=143.4

Q ss_pred             eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013           13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII   68 (167)
Q Consensus        13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l   68 (167)
                      .|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++|+.|+++++++|
T Consensus         1 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L   80 (174)
T cd04518           1 SLKIENIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKL   80 (174)
T ss_pred             CcEEEEEEEEEEcCCeecHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999999998                        9999999999999999999999


Q ss_pred             HhcCCCCc-ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHH
Q 031013           69 QKLGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE  147 (167)
Q Consensus        69 ~~lg~~~~-~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~  147 (167)
                      +++|++.. ..+|+|+|||||++++++|||+.++..++ +++||||+||||+||+.+|+++++||+||||+||||||++|
T Consensus        81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~~~-~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~  159 (174)
T cd04518          81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLP-NAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEED  159 (174)
T ss_pred             HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhhCC-CCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHH
Confidence            99999864 56899999999999999999999999885 99999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 031013          148 TYTAFENIYPVLTEF  162 (167)
Q Consensus       148 ~~~a~~~i~~~L~~~  162 (167)
                      +++|++++++.|+++
T Consensus       160 ~~~a~~~i~~~l~~~  174 (174)
T cd04518         160 AKRAVEKLLSRLKEL  174 (174)
T ss_pred             HHHHHHHHHHHHhhC
Confidence            999999999999864

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.

>PRK00394 transcription factor; Reviewed

Probab=100.00  E-value=1.5e-54  Score=347.52  Aligned_cols=151  Identities=42%  Similarity=0.685  Sum_probs=144.9

Q ss_pred             eEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHHHh
Q 031013           15 SVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARIIQK   70 (167)
Q Consensus        15 ~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l~~   70 (167)
                      +|+|||||++++|+|||++||..++|++|||+                        +||||+|+++|+.|+++++++|++
T Consensus         2 ~i~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l~~   81 (179)
T PRK00394          2 KIENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKLKE   81 (179)
T ss_pred             EEEEEEEEEEcCCCcCHHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999999998                        899999999999999999999999


Q ss_pred             cCCCCc-ccceEEEEEEEEEecCCccchHhHHHHcC-CCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013           71 LGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHG-AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET  148 (167)
Q Consensus        71 lg~~~~-~~~~~I~NIvas~~l~~~I~L~~la~~~~-~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~  148 (167)
                      +|+++. ..+|+|+|||||+|++++|||+++|..++ ++++||||+||||+||+.+|+++++||+||||+||||||++|+
T Consensus        82 ~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~  161 (179)
T PRK00394         82 LGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDA  161 (179)
T ss_pred             cCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHH
Confidence            999875 67999999999999999999999998863 5899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhhh
Q 031013          149 YTAFENIYPVLTEFRKV  165 (167)
Q Consensus       149 ~~a~~~i~~~L~~~r~~  165 (167)
                      ++|+++|+|+|+++...
T Consensus       162 ~~a~~~i~~~l~~~g~~  178 (179)
T PRK00394        162 EKAVEKILEKLEELGLL  178 (179)
T ss_pred             HHHHHHHHHHHHHcCCc
Confidence            99999999999998653

>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

Probab=100.00  E-value=3.9e-54  Score=343.63  Aligned_cols=149  Identities=72%  Similarity=1.154  Sum_probs=144.5

Q ss_pred             eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013           13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII   68 (167)
Q Consensus        13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l   68 (167)
                      .|+|+||||+++++|+|||++||..++|++|||+                        +||||+|+++++.|+++++++|
T Consensus         1 ~~~i~NvVas~~l~~~idL~~la~~~~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L   80 (174)
T cd00652           1 SPKIQNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARIL   80 (174)
T ss_pred             CcEEEEEEEEEEcCCccCHHHHHhhCCCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence            3799999999999999999999999999999997                        9999999999999999999999


Q ss_pred             HhcCCCC-cccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHH
Q 031013           69 QKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE  147 (167)
Q Consensus        69 ~~lg~~~-~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~  147 (167)
                      +++|++. ++.+|+|+|||||+++|++|||++||..++++++||||+||||+||+.+|++|++||+||||+||||||++|
T Consensus        81 ~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~  160 (174)
T cd00652          81 QKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSRED  160 (174)
T ss_pred             HHcCCCccccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence            9999986 889999999999999999999999999986799999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 031013          148 TYTAFENIYPVLTE  161 (167)
Q Consensus       148 ~~~a~~~i~~~L~~  161 (167)
                      +++|+++|+|+|.+
T Consensus       161 ~~~a~~~i~~~L~~  174 (174)
T cd00652         161 IYEAVEKIYPILKE  174 (174)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999999974

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many

>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans

Probab=100.00  E-value=1.4e-53  Score=340.65  Aligned_cols=149  Identities=44%  Similarity=0.841  Sum_probs=144.4

Q ss_pred             eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC-----------------------ceeccCCHHHHHHHHHHHHHHHH
Q 031013           13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK-----------------------VCTGAKSEQQSKLAARKYARIIQ   69 (167)
Q Consensus        13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~-----------------------v~tGakS~~~a~~a~~k~~~~l~   69 (167)
                      .++|+|||||++++|+|||++++..++|+||||+                       +|||++|+++|+.|+++++++|+
T Consensus         2 ~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l~   81 (174)
T cd04517           2 DILIVNVVCQFSLRCHIDLRKLALAGRNVEYNPRYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLLQ   81 (174)
T ss_pred             ccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeCCCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999999998                       89999999999999999999999


Q ss_pred             hcCCCC-cccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013           70 KLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET  148 (167)
Q Consensus        70 ~lg~~~-~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~  148 (167)
                      ++|++. ++.+|+|+|||||+|+|++|||++|+..+.++++||||+||||+||+.+|++|++||+||||+|||+||++|+
T Consensus        82 ~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~  161 (174)
T cd04517          82 KLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDV  161 (174)
T ss_pred             HcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHH
Confidence            999986 8899999999999999999999999998767999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 031013          149 YTAFENIYPVLTE  161 (167)
Q Consensus       149 ~~a~~~i~~~L~~  161 (167)
                      ++|+++|+|+|.+
T Consensus       162 ~~a~~~i~pil~~  174 (174)
T cd04517         162 REAVEKIYPIVFE  174 (174)
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999999864

TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.

>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]

Probab=100.00  E-value=3.8e-33  Score=199.12  Aligned_cols=86  Identities=56%  Similarity=0.864  Sum_probs=81.1

Q ss_pred             ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013           77 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY  156 (167)
Q Consensus        77 ~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~  156 (167)
                      |++|+|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||||++++++|+++++
T Consensus         1 ~~~~~i~NIva~~~l~~~idL~~la~~~-~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~   79 (86)
T PF00352_consen    1 FPDFKIVNIVASFDLPFEIDLEELAEEL-ENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKIL   79 (86)
T ss_dssp             -EEEEEEEEEEEEE-SSEB-HHHHHHHS-TTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCccEEEEEEEEEECCCccCHHHHHhhc-cCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHH
Confidence            5789999999999999999999999998 799999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhh
Q 031013          157 PVLTEFR  163 (167)
Q Consensus       157 ~~L~~~r  163 (167)
                      |+|++++
T Consensus        80 ~~L~~~~   86 (86)
T PF00352_consen   80 PILQKLG   86 (86)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHcC
Confidence            9999985

TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....

>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

Probab=99.96  E-value=7.7e-29  Score=198.13  Aligned_cols=83  Identities=34%  Similarity=0.541  Sum_probs=79.8

Q ss_pred             eEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013           80 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL  159 (167)
Q Consensus        80 ~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L  159 (167)
                      ++|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+++++||+||||+||||||+|+++.|+++++++|
T Consensus         2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L   80 (174)
T cd04516           2 PKIQNIVATVNLGCKLDLKKIALRA-RNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII   80 (174)
T ss_pred             CEEEEEEEEEEcCCeecHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence            6899999999999999999999887 689999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhh
Q 031013          160 TEFR  163 (167)
Q Consensus       160 ~~~r  163 (167)
                      +++-
T Consensus        81 ~~~g   84 (174)
T cd04516          81 QKLG   84 (174)
T ss_pred             HHcC
Confidence            8764

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.

>PLN00062 TATA-box-binding protein; Provisional

Probab=99.96  E-value=1.2e-28  Score=197.81  Aligned_cols=83  Identities=30%  Similarity=0.518  Sum_probs=79.7

Q ss_pred             eEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013           80 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL  159 (167)
Q Consensus        80 ~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L  159 (167)
                      ++|+|||||++++++|||++|+..+ ++++||||+|||++||+.+|+++++||+||||+||||||+++++.|++++.++|
T Consensus         2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L   80 (179)
T PLN00062          2 PTLQNIVSTVNLDCKLDLKKIALQA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII   80 (179)
T ss_pred             cEEEEEEEEEEcCCcccHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence            6899999999999999999999877 589999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhh
Q 031013          160 TEFR  163 (167)
Q Consensus       160 ~~~r  163 (167)
                      +++-
T Consensus        81 ~~lg   84 (179)
T PLN00062         81 QKLG   84 (179)
T ss_pred             HHcC
Confidence            8764

>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription

Probab=99.95  E-value=3.1e-28  Score=194.65  Aligned_cols=84  Identities=42%  Similarity=0.682  Sum_probs=80.3

Q ss_pred             ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013           79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV  158 (167)
Q Consensus        79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~  158 (167)
                      .++|+|||||++++++|||++|+..+ ++++||||+|||++||+.+|+++++||+||||+||||||+++++.|++++.++
T Consensus         1 ~~~I~NvVas~~l~~~ldL~~la~~~-~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~   79 (174)
T cd04518           1 SLKIENIVASVDLGQELDLEKVAAEL-PNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKK   79 (174)
T ss_pred             CcEEEEEEEEEEcCCeecHHHHHhhC-CCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence            36899999999999999999999987 68999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhh
Q 031013          159 LTEFR  163 (167)
Q Consensus       159 L~~~r  163 (167)
                      |+++-
T Consensus        80 L~~~g   84 (174)
T cd04518          80 LKDYG   84 (174)
T ss_pred             HHhcC
Confidence            98753

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.

>PRK00394 transcription factor; Reviewed

Probab=99.95  E-value=3e-28  Score=195.49  Aligned_cols=83  Identities=45%  Similarity=0.665  Sum_probs=79.5

Q ss_pred             eEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013           80 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL  159 (167)
Q Consensus        80 ~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L  159 (167)
                      ++|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||+|+++++.|++++.++|
T Consensus         1 i~i~NvVas~~l~~~ldL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l   79 (179)
T PRK00394          1 IKIENIVASTDLGQELDLEKVAEDL-PNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKL   79 (179)
T ss_pred             CEEEEEEEEEEcCCCcCHHHHHhhC-CCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHH
Confidence            4899999999999999999999887 599999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhh
Q 031013          160 TEFR  163 (167)
Q Consensus       160 ~~~r  163 (167)
                      +++-
T Consensus        80 ~~~g   83 (179)
T PRK00394         80 KELG   83 (179)
T ss_pred             HHcC
Confidence            8763

>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

Probab=99.95  E-value=1.5e-28  Score=195.11  Aligned_cols=84  Identities=39%  Similarity=0.613  Sum_probs=80.4

Q ss_pred             cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013           78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP  157 (167)
Q Consensus        78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~  157 (167)
                      ..++|+|||||.+++.++||++++..+ ++++||||+||||+||+.+||+++|||+|||+|||||||.++++.|++++..
T Consensus         6 ~~i~IeNIVAS~~L~~elDL~~~~~~l-~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~~   84 (185)
T COG2101           6 PTITIENIVASVDLGQELDLEEVALDL-PGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLAK   84 (185)
T ss_pred             CccEEEEEEEEechhhhccHHHHHhhC-CCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHHH
Confidence            468999999999999999999999988 6999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q 031013          158 VLTEF  162 (167)
Q Consensus       158 ~L~~~  162 (167)
                      .|++.
T Consensus        85 ~L~~~   89 (185)
T COG2101          85 KLKDG   89 (185)
T ss_pred             HHHhc
Confidence            98863

>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription

Probab=99.95  E-value=4.6e-28  Score=193.46  Aligned_cols=84  Identities=37%  Similarity=0.606  Sum_probs=80.4

Q ss_pred             ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013           79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV  158 (167)
Q Consensus        79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~  158 (167)
                      +++|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||+|+++++.|++++.++
T Consensus         1 ~~~i~NvVas~~l~~~idL~~la~~~-~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~   79 (174)
T cd00652           1 SPKIQNIVATVNLGCELDLRKIALAA-RNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARI   79 (174)
T ss_pred             CcEEEEEEEEEEcCCccCHHHHHhhC-CCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHH
Confidence            47899999999999999999999987 59999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhh
Q 031013          159 LTEFR  163 (167)
Q Consensus       159 L~~~r  163 (167)
                      |+++-
T Consensus        80 L~~~g   84 (174)
T cd00652          80 LQKLG   84 (174)
T ss_pred             HHHcC
Confidence            98764

TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many

>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans

Probab=99.94  E-value=4.7e-27  Score=187.79  Aligned_cols=83  Identities=29%  Similarity=0.470  Sum_probs=79.7

Q ss_pred             ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013           79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV  158 (167)
Q Consensus        79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~  158 (167)
                      +++|+|||||++++++|||++++..+ ++++||| +||||+||+.+|+++++||+|||++|||+||++++++|++++.++
T Consensus         2 ~~~i~Nvvas~~l~~~idL~~la~~l-~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~   79 (174)
T cd04517           2 DILIVNVVCQFSLRCHIDLRKLALAG-RNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARL   79 (174)
T ss_pred             ccEEEEEEEEEEcCCcccHHHHHhhC-CCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence            68999999999999999999999887 6999999 999999999999999999999999999999999999999999999


Q ss_pred             HHhhh
Q 031013          159 LTEFR  163 (167)
Q Consensus       159 L~~~r  163 (167)
                      |+++-
T Consensus        80 l~~~g   84 (174)
T cd04517          80 LQKLG   84 (174)
T ss_pred             HHHcC
Confidence            98764

TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.

>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

Probab=99.86  E-value=2.1e-21  Score=156.53  Aligned_cols=84  Identities=33%  Similarity=0.521  Sum_probs=80.7

Q ss_pred             cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013           78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP  157 (167)
Q Consensus        78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~  157 (167)
                      .++.++||||++++++++||.+||... .|++|||+.|++++.|+.+|+++++||+||||+||||+|+++++.|..++.+
T Consensus        21 i~~~l~nivc~~~~~c~ldLk~ial~~-~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~aR   99 (200)
T KOG3302|consen   21 LDPTLQNIVCTVNLNCKLDLKEIALHA-RNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYAR   99 (200)
T ss_pred             cceEEEeEEEEEeccceecHHHHhhhc-cccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHHH
Confidence            368899999999999999999999975 6999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q 031013          158 VLTEF  162 (167)
Q Consensus       158 ~L~~~  162 (167)
                      +|+++
T Consensus       100 ilqkL  104 (200)
T KOG3302|consen  100 ILQKL  104 (200)
T ss_pred             HHHHc
Confidence            99976

>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]

Probab=99.73  E-value=1e-17  Score=119.43  Aligned_cols=60  Identities=43%  Similarity=0.622  Sum_probs=56.4

Q ss_pred             eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013           13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII   68 (167)
Q Consensus        13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l   68 (167)
                      .++|+||||+++++++|||.+||..++|++|||+                        +||||+|+++++.|++++.++|
T Consensus         3 ~~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L   82 (86)
T PF00352_consen    3 DFKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPIL   82 (86)
T ss_dssp             EEEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             ccEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999                        8999999999999999999999


Q ss_pred             HhcC
Q 031013           69 QKLG   72 (167)
Q Consensus        69 ~~lg   72 (167)
                      +++|
T Consensus        83 ~~~~   86 (86)
T PF00352_consen   83 QKLG   86 (86)
T ss_dssp             HHTT
T ss_pred             HHcC
Confidence            9987

TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....

>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3

Probab=96.85  E-value=0.0013  Score=46.68  Aligned_cols=36  Identities=22%  Similarity=0.413  Sum_probs=30.5

Q ss_pred             CCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013          113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET  148 (167)
Q Consensus       113 E~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~  148 (167)
                      ..=||.+|+...+.+++++|.||||++-|...+.++
T Consensus        26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~A   61 (81)
T PF11858_consen   26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQEA   61 (81)
T ss_dssp             S--TTEEEEEEETTEEEEEETTSEEEEESTTHHHHH
T ss_pred             CCCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHHH
Confidence            344999999999999999999999999998766544

1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.

>COG4871 Uncharacterized protein conserved in archaea [Function unknown]

Probab=95.50  E-value=0.1  Score=42.02  Aligned_cols=73  Identities=22%  Similarity=0.252  Sum_probs=58.0

Q ss_pred             EEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHh
Q 031013           85 IVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTE  161 (167)
Q Consensus        85 Ivas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~  161 (167)
                      |.|..|-+++==|.-|+..+ +.+.|.... ..|++..-+  .-+.||.||||.+|--|+++++++.+..+..++.+
T Consensus        36 Vi~~md~~lg~ilplla~l~-P~anY~~kk-~~l~~~kge--rIitiy~sGkVsm~~ikdedEAkeilgel~d~ine  108 (193)
T COG4871          36 VIANMDPPLGGILPLLAPLF-PRANYSDKK-NILILQKGE--RIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE  108 (193)
T ss_pred             EEeecCCCcchhHHHhHhhC-CCccccccc-ceEEEeecc--EEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence            45556666666677888887 469998654 778887554  44679999999999999999999999999888765

>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]

Probab=94.90  E-value=0.078  Score=45.94  Aligned_cols=44  Identities=25%  Similarity=0.360  Sum_probs=37.8

Q ss_pred             CCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013          113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY  156 (167)
Q Consensus       113 E~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~  156 (167)
                      .+.|+.+|+.+.|.+++.+|.|||+++-|-..++.+++-...+.
T Consensus        27 ~~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~   70 (297)
T COG1039          27 SNPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIA   70 (297)
T ss_pred             cCCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhh
Confidence            47799999999999999999999999999988877776665433

>PRK00996 ribonuclease HIII; Provisional

Probab=94.26  E-value=0.09  Score=45.62  Aligned_cols=34  Identities=32%  Similarity=0.700  Sum_probs=29.7

Q ss_pred             cCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013          112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR  145 (167)
Q Consensus       112 PE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~  145 (167)
                      +..-|+..|+...+.+++.+|.||||++.|...+
T Consensus        26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae   59 (304)
T PRK00996         26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE   59 (304)
T ss_pred             cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence            4456899999999999999999999999996544

>TIGR00716 rnhC ribonuclease HIII

Probab=94.03  E-value=0.13  Score=44.23  Aligned_cols=34  Identities=21%  Similarity=0.448  Sum_probs=29.8

Q ss_pred             ccCCCCeEEEEEcCCeEEEEEecCceEEEEccCC
Q 031013          111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKV  144 (167)
Q Consensus       111 ePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks  144 (167)
                      .+..=||.+|+...+.+|+.+|.||||++-|...
T Consensus        22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~a   55 (284)
T TIGR00716        22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNS   55 (284)
T ss_pred             ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCH
Confidence            4555799999999999999999999999999443

Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.

>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional

Probab=84.52  E-value=3.4  Score=36.22  Aligned_cols=36  Identities=14%  Similarity=0.406  Sum_probs=29.1

Q ss_pred             EEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHH
Q 031013          118 LIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENI  155 (167)
Q Consensus       118 lv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i  155 (167)
                      +.|+..+  -.+.+|.+|++.|-|.+++.+++.-+.+.
T Consensus       301 ~~~~~~~--~~~~~f~~gr~~~~g~~~~~~a~~~~~~~  336 (338)
T PRK12475        301 LSFQLDE--YRFVLFTDGRAFIHGTNDIKKAKRLYARY  336 (338)
T ss_pred             EEEEECC--EEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence            3456555  56789999999999999999998877664

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	167
1vto_A	190	1.9 A Resolution Refined Structure Of Tbp Recognizi		4e-76
1vok_A	200	Arabidopsis Thaliana Tbp (Dimer) Length = 200		4e-76
1vtl_E	186	Co-Crystal Structure Of Tbp Recognizing The Minor G		7e-75
1jfi_C	185	Crystal Structure Of The Nc2-Tbp-Dna Ternary Comple		9e-67
1nvp_A	181	Human TfiiaTBPDNA COMPLEX Length = 181		1e-66
1tgh_A	185	Tata Binding Protein (Tbp)DNA COMPLEX Length = 185		1e-66
1c9b_B	180	Crystal Structure Of A Human Tbp Core Domain-Human		2e-66
1tbp_A	180	Crystal Structure Of Yeast Tata-Binding Protein And		2e-66
1rm1_A	240	Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex L		2e-66
1ytb_A	180	Crystal Structure Of A Yeast TbpTATA-Box Complex Le		4e-66
1cdw_A	179	Human Tbp Core Domain Complexed With Dna Length = 1		6e-66
3oc3_C	218	Crystal Structure Of The Mot1 N-Terminal Domain In		1e-60
3eik_A	218	Double Stranded Dna Binding Protein Length = 218		1e-60
1mp9_A	198	Tbp From A Mesothermophilic Archaeon, Sulfolobus Ac		2e-23
2z8u_A	188	Methanococcus Jannaschii Tbp Length = 188		2e-20
1ais_A	182	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-		7e-18
1pcz_A	191	Structure Of Tata-Binding Protein Length = 191		7e-18
1d3u_A	181	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T		8e-18

>pdb|1VTO|A Chain A, 1.9 A Resolution Refined Structure Of Tbp Recognizing The Minor Groove Of Tataaaag Length = 190

Iteration: 1
 Score =  280 bits (715), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 141/181 (77%), Positives = 149/181 (82%), Gaps = 24/181 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 10  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 69
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE  SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 70  VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 129
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+Q
Sbjct: 130 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 189
Query: 167 Q 167
           Q
Sbjct: 190 Q 190

>pdb|1VOK|A Chain A, Arabidopsis Thaliana Tbp (Dimer) Length = 200

Iteration: 1
 Score =  280 bits (715), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 141/181 (77%), Positives = 149/181 (82%), Gaps = 24/181 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 20  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE  SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 80  VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 139
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+Q
Sbjct: 140 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 199
Query: 167 Q 167
           Q
Sbjct: 200 Q 200

>pdb|1VTL|E Chain E, Co-Crystal Structure Of Tbp Recognizing The Minor Groove Of A Tata Element Length = 186

Iteration: 1
 Score =  275 bits (704), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 139/179 (77%), Positives = 147/179 (82%), Gaps = 24/179 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 8   GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 67
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE  SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 68  VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 127
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+
Sbjct: 128 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 186

>pdb|1JFI|C Chain C, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex Length = 185

Iteration: 1
 Score =  248 bits (634), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 6   GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 65
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct: 66  VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 125
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct: 126 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 183

>pdb|1NVP|A Chain A, Human TfiiaTBPDNA COMPLEX Length = 181

Iteration: 1
 Score =  248 bits (633), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 2   GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 61
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct: 62  VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 121
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct: 122 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 179

>pdb|1TGH|A Chain A, Tata Binding Protein (Tbp)DNA COMPLEX Length = 185

Iteration: 1
 Score =  248 bits (632), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 6   GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 65
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct: 66  VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 125
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct: 126 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 183

>pdb|1C9B|B Chain B, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib Core Domain Complex Bound To An Extended, Modified Adenoviral Major Late Promoter (Admlp) Length = 180

Iteration: 1
 Score =  248 bits (632), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 3   GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 62
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct: 63  VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 122
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct: 123 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 180

>pdb|1TBP|A Chain A, Crystal Structure Of Yeast Tata-Binding Protein And Model For Interaction With Dna Length = 180

Iteration: 1
 Score =  248 bits (632), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/180 (68%), Positives = 139/180 (77%), Gaps = 24/180 (13%)
Query: 10  LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK----------------------- 46
           +G V +++NIV+TV L C+LDLK +AL ARNAEYNPK                       
Sbjct: 1   MGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK 60
Query: 47  -VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHG 105
            V TGAKSE  SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG
Sbjct: 61  MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG 120
Query: 106 AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
            FSSYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 121 TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 180

>pdb|1RM1|A Chain A, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex Length = 240

Iteration: 1
 Score =  247 bits (630), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/179 (69%), Positives = 138/179 (77%), Gaps = 24/179 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIV+TV L C+LDLK +AL ARNAEYNPK                        
Sbjct: 62  GIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 121
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           V TGAKSE  SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG 
Sbjct: 122 VVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGT 181
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           FSSYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 182 FSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 240

>pdb|1YTB|A Chain A, Crystal Structure Of A Yeast TbpTATA-Box Complex Length = 180

Iteration: 1
 Score =  246 bits (629), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 124/179 (69%), Positives = 138/179 (77%), Gaps = 24/179 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V +++NIV+TV L C+LDLK +AL ARNAEYNPK                        
Sbjct: 2   GIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 61
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           V TGAKSE  SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG 
Sbjct: 62  VVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGT 121
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           FSSYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 122 FSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 180

>pdb|1CDW|A Chain A, Human Tbp Core Domain Complexed With Dna Length = 179

Iteration: 1
 Score =  246 bits (627), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 123/178 (69%), Positives = 137/178 (76%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G V  ++NIVSTVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 2   GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 61
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           VCTGAKSE+ S+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL  +H  
Sbjct: 62  VCTGAKSEENSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 121
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L  FRK
Sbjct: 122 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 179

>pdb|3OC3|C Chain C, Crystal Structure Of The Mot1 N-Terminal Domain In Complex With Tbp Length = 218

Iteration: 1
 Score =  228 bits (581), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 113/178 (63%), Positives = 133/178 (74%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++N+V+TVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 40  GIIPTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 99
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           V TGAKSE+ S++AA++YA+II KLGF A F DFKIQNIV SCD+KF IRLEGLAY+H  
Sbjct: 100 VITGAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSN 159
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           + SYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAKVRD+ Y AF NIYPVL + RK
Sbjct: 160 YCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVLIQHRK 217

>pdb|3EIK|A Chain A, Double Stranded Dna Binding Protein Length = 218

Iteration: 1
 Score =  228 bits (581), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 113/178 (63%), Positives = 133/178 (74%), Gaps = 24/178 (13%)
Query: 11  GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
           G + +++N+V+TVNL CKLDLK IAL+ARNAEYNPK                        
Sbjct: 40  GIIPTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 99
Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
           V TGAKSE+ S++AA++YA+II KLGF A F DFKIQNIV SCD+KF IRLEGLAY+H  
Sbjct: 100 VITGAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSN 159
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           + SYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAKVRD+ Y AF NIYPVL + RK
Sbjct: 160 YCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVLIQHRK 217

>pdb|1MP9|A Chain A, Tbp From A Mesothermophilic Archaeon, Sulfolobus Acidocaldarius Length = 198

Iteration: 1
 Score =  105 bits (261), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 67/176 (38%), Positives = 93/176 (52%), Gaps = 26/176 (14%)
Query: 12  AVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------V 47
           AV +++NIV+TV LD  LDL  +     N EY+P                         V
Sbjct: 11  AVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMV 70
Query: 48  CTGAKSEQQSKLAARKYARIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
            TGAKS  +   A ++  + ++K G     K   +IQNIV S ++   + L+  A+    
Sbjct: 71  VTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLEN 130
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
            + YEPE FPGLIYRM +P++VLLIF SGK+VITGAK  DE + A + I+  L E 
Sbjct: 131 -NMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVEL 185

>pdb|2Z8U|A Chain A, Methanococcus Jannaschii Tbp Length = 188

Iteration: 1
 Score = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 93/173 (53%), Gaps = 26/173 (15%)
Query: 18  NIVSTVNLDCKLDLKKIALQARNAEYNPKV------------------------CTGAKS 53
           N+V +  +   +DL+++A+   NAEY P+                         CTGAKS
Sbjct: 17  NVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKS 76
Query: 54  EQQSKLAARKYARIIQKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEP 112
           ++++++A +K  + ++  G    +  + KIQN+V + D+     L+ +A      + YEP
Sbjct: 77  KEEAEIAIKKIIKELKDAGIDVIENPEIKIQNMVATADLGIEPNLDDIALMVEG-TEYEP 135
Query: 113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           E FPGL+YR+  PK+V+LIF SGK+VITG K  ++   A + I   + E +++
Sbjct: 136 EQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKILDTIKEVQEL 188

>pdb|1AIS|A Chain A, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box Complex From Pyrococcus Woesei Length = 182

Iteration: 1
 Score = 86.3 bits (212), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 60/174 (34%), Positives = 93/174 (53%), Gaps = 30/174 (17%)
Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++V+L  +LDL+K+     N++YNP+                        V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
           KS Q  + A  K A+ ++ +G   KFK      +QN+V S D+     L+ +A +     
Sbjct: 71  KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPN-C 127
Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
            YEPE FPG+IYR+K+PK V+L+F SGKIV +GAK   + + A   +   L ++
Sbjct: 128 EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181

>pdb|1PCZ|A Chain A, Structure Of Tata-Binding Protein Length = 191

Iteration: 1
 Score = 86.3 bits (212), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 60/174 (34%), Positives = 93/174 (53%), Gaps = 30/174 (17%)
Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++V+L  +LDL+K+     N++YNP+                        V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
           KS Q  + A  K A+ ++ +G   KFK      +QN+V S D+     L+ +A +     
Sbjct: 71  KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPN-C 127
Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
            YEPE FPG+IYR+K+PK V+L+F SGKIV +GAK   + + A   +   L ++
Sbjct: 128 EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181

>pdb|1D3U|A Chain A, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA- Box Complex From Pyrococcus Woesei Length = 181

Iteration: 1
 Score = 86.3 bits (212), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 60/174 (34%), Positives = 93/174 (53%), Gaps = 30/174 (17%)
Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++V+L  +LDL+K+     N++YNP+                        V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
           KS Q  + A  K A+ ++ +G   KFK      +QN+V S D+     L+ +A +     
Sbjct: 71  KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPN-C 127
Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
            YEPE FPG+IYR+K+PK V+L+F SGKIV +GAK   + + A   +   L ++
Sbjct: 128 EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	167
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	2e-64
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	2e-20
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	1e-62
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	5e-23
1ytb_A	180	Protein (tata binding protein (TBP)); protein-DNA	6e-60
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	4e-59
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	4e-20
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	7e-59
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	2e-19
1mp9_A	198	Tata-binding protein; transcription regulation, DN	1e-58
1mp9_A	198	Tata-binding protein; transcription regulation, DN	8e-20
1mp9_A	198	Tata-binding protein; transcription regulation, DN	3e-06

>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C Length = 218

 Score =  196 bits (498), Expect = 2e-64
 Identities = 112/173 (64%), Positives = 130/173 (75%), Gaps = 24/173 (13%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++N+V+TVNL CKLDLK IAL+ARNAEYNPK                        V TGA
Sbjct: 45  LQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGA 104

Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYE 111
           KSE+ S++AA++YA+II KLGF A F DFKIQNIV SCD+KF IRLEGLAY+H  + SYE
Sbjct: 105 KSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSNYCSYE 164

Query: 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
           PELFPGLIYRM +PKIVLLIFVSGKIV+TGAKVRD+ Y AF NIYPVL + RK
Sbjct: 165 PELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVLIQHRK 217

>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C Length = 218

 Score = 83.2 bits (205), Expect = 2e-20
 Identities = 29/117 (24%), Positives = 54/117 (46%), Gaps = 2/117 (1%)

Query: 48  CTGAKSEQQSKLAARKYARIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
            +G        + A   +   Q+   P +      +QN+V + ++   + L+ +A     
Sbjct: 10  SSGLVPRGSHMMDAPDISYEHQETSVPNRSGIIPTLQNVVATVNLSCKLDLKNIA-LRAR 68

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFR 163
            + Y P+ F  +I R+++PK   LIF SGK+VITGAK    +  A +    ++ +  
Sbjct: 69  NAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGAKSEKSSRMAAQRYAKIIHKLG 125

>1rm1_A Tata-box binding protein; yeast TFIIA, TBP protein, ATA-box DNA, transcription/DNA complex; 2.50A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1 Length = 240

 Score =  192 bits (488), Expect = 1e-62
 Identities = 122/174 (70%), Positives = 135/174 (77%), Gaps = 24/174 (13%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV+TV L C+LDLK +AL ARNAEYNPK                        V TGA
Sbjct: 67  LQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGA 126

Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYE 111
           KSE  SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG FSSYE
Sbjct: 127 KSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYE 186

Query: 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           PELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 187 PELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 240

>1rm1_A Tata-box binding protein; yeast TFIIA, TBP protein, ATA-box DNA, transcription/DNA complex; 2.50A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1 Length = 240

 Score = 90.2 bits (223), Expect = 5e-23
 Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 5/113 (4%)

Query: 47  VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
             T  +SE+  K AA +  +               +QNIV +  +   + L+ +A  H  
Sbjct: 36  PATTFQSEEDIKRAAPESEKDTSATSGI----VPTLQNIVATVTLGCRLDLKTVA-LHAR 90

Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 159
            + Y P+ F  +I R+++PK   LIF SGK+V+TGAK  D++  A      ++
Sbjct: 91  NAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARII 143

>1ytb_A Protein (tata binding protein (TBP)); protein-DNA complex, transcription/DNA complex; HET: DNA; 1.80A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1 PDB: 1ngm_A* 1tba_B 1nh2_A* 1ytf_A* 1tbp_A 1qna_A* 1qn3_A* 1qn5_A* 1qn6_A* 1qn7_A* 1qn8_A* 1qn9_A* 1qn4_A* 1qnb_A* 1qnc_A* 1qne_A* 1vok_A 1vol_B* 1vto_A* 1vtl_E* ... Length = 180

 Score =  183 bits (465), Expect = 6e-60
 Identities = 122/175 (69%), Positives = 136/175 (77%), Gaps = 24/175 (13%)

Query: 15  SVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTG 50
           +++NIV+TV L C+LDLK +AL ARNAEYNPK                        V TG
Sbjct: 6   TLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTG 65

Query: 51  AKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSY 110
           AKSE  SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG FSSY
Sbjct: 66  AKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSY 125

Query: 111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           EPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 126 EPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 180

>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein, transcription factor, transcription regulation; 1.90A {Methanococcus jannaschii} Length = 188

 Score =  181 bits (460), Expect = 4e-59
 Identities = 54/175 (30%), Positives = 94/175 (53%), Gaps = 26/175 (14%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           + N+V +  +   +DL+++A+   NAEY P+                         CTGA
Sbjct: 15  IVNVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGA 74

Query: 52  KSEQQSKLAARKYARIIQKLGFP-AKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSY 110
           KS++++++A +K  + ++  G    +  + KIQN+V + D+     L+ +A      + Y
Sbjct: 75  KSKEEAEIAIKKIIKELKDAGIDVIENPEIKIQNMVATADLGIEPNLDDIALMVE-GTEY 133

Query: 111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
           EPE FPGL+YR+  PK+V+LIF SGK+VITG K  ++   A + I   + E +++
Sbjct: 134 EPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKILDTIKEVQEL 188

>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein, transcription factor, transcription regulation; 1.90A {Methanococcus jannaschii} Length = 188

 Score = 81.6 bits (201), Expect = 4e-20
 Identities = 35/84 (41%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
           + KI N+V S  +   I LE +A      + YEPE FPGL+ R+  PK+ LLIF SGK+ 
Sbjct: 12  EIKIVNVVVSTKIGDNIDLEEVA-MILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVN 70

Query: 139 ITGAKVRDETYTAFENIYPVLTEF 162
            TGAK ++E   A + I   L + 
Sbjct: 71  CTGAKSKEEAEIAIKKIIKELKDA 94

>1ais_A TBP, protein (tata-binding protein); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: d.129.1.1 d.129.1.1 PDB: 1d3u_A* 1pcz_A Length = 182

 Score =  180 bits (458), Expect = 7e-59
 Identities = 58/172 (33%), Positives = 91/172 (52%), Gaps = 26/172 (15%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++V+L  +LDL+K+     N++YNP+                        V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70

Query: 52  KSEQQSKLAARKYARIIQKLGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSY 110
           KS Q  + A  K A+ ++ +G   K      +QN+V S D+     L+ +A +      Y
Sbjct: 71  KSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLP-NCEY 129

Query: 111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
           EPE FPG+IYR+K+PK V+L+F SGKIV +GAK   + + A   +   L ++
Sbjct: 130 EPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181

>1ais_A TBP, protein (tata-binding protein); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: d.129.1.1 d.129.1.1 PDB: 1d3u_A* 1pcz_A Length = 182

 Score = 79.7 bits (196), Expect = 2e-19
 Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
             +I+NIV S D+   + LE +       S Y PE FPG+I  +  PK+ LLIF SGK+V
Sbjct: 8   KLRIENIVASVDLFAQLDLEKVL-DLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLV 66

Query: 139 ITGAKVRDETYTAFENIYPVLTEF 162
           +TGAK   +   A   +   L   
Sbjct: 67  VTGAKSVQDIERAVAKLAQKLKSI 90

>1mp9_A Tata-binding protein; transcription regulation, DNA-binding protein, transcription factor, DNA binding protein; 2.00A {Sulfolobus acidocaldarius} SCOP: d.129.1.1 d.129.1.1 Length = 198

 Score =  180 bits (457), Expect = 1e-58
 Identities = 65/178 (36%), Positives = 92/178 (51%), Gaps = 26/178 (14%)

Query: 15  SVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTG 50
           +++NIV+TV LD  LDL  +     N EY+P                         V TG
Sbjct: 14  NIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTG 73

Query: 51  AKSEQQSKLAARKYARIIQKLGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSS 109
           AKS  +   A ++  + ++K G         +IQNIV S ++   + L+  A+     + 
Sbjct: 74  AKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLE-NNM 132

Query: 110 YEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ 167
           YEPE FPGLIYRM +P++VLLIF SGK+VITGAK  DE + A + I+  L E   V+ 
Sbjct: 133 YEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVELDCVKP 190

>1mp9_A Tata-binding protein; transcription regulation, DNA-binding protein, transcription factor, DNA binding protein; 2.00A {Sulfolobus acidocaldarius} SCOP: d.129.1.1 d.129.1.1 Length = 198

 Score = 80.8 bits (199), Expect = 8e-20
 Identities = 32/84 (38%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
              I+NIV +  +   + L  +         Y+P+ FPGLI+R++ PKI  LIF SGK+V
Sbjct: 12  VVNIENIVATVTLDQTLDLYAME-RSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMV 70

Query: 139 ITGAKVRDETYTAFENIYPVLTEF 162
           +TGAK  DE   A + I   L ++
Sbjct: 71  VTGAKSTDELIKAVKRIIKTLKKY 94

>1mp9_A Tata-binding protein; transcription regulation, DNA-binding protein, transcription factor, DNA binding protein; 2.00A {Sulfolobus acidocaldarius} SCOP: d.129.1.1 d.129.1.1 Length = 198

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 24/92 (26%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++ NL   ++L K A    N  Y P+                        V TGA
Sbjct: 106 IQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGA 165

Query: 52  KSEQQSKLAARKYARIIQKLGFPAKFKDFKIQ 83
           K E +   A +K    + +L      ++ +++
Sbjct: 166 KREDEVHKAVKKIFDKLVELDCVKPVEEEELE 197

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	167
1ytb_A	180	Protein (tata binding protein (TBP)); protein-DNA	100.0
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	100.0
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	100.0
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	100.0
1mp9_A	198	Tata-binding protein; transcription regulation, DN	100.0
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	100.0
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	100.0
1ytb_A	180	Protein (tata binding protein (TBP)); protein-DNA	99.96
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	99.95
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	99.95
1mp9_A	198	Tata-binding protein; transcription regulation, DN	99.95
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	99.95
3vn5_A	257	RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {A	93.82
2d0b_A	310	RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd	93.65
2ctf_A	102	Vigilin; K homology type I domain, RNA-binding, ce	81.72

>1ytb_A Protein (tata binding protein (TBP)); protein-DNA complex, transcription/DNA complex; HET: DNA; 1.80A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1 PDB: 1ngm_A* 1tba_B 1nh2_A* 1ytf_A* 1tbp_A 1qna_A* 1qn3_A* 1qn5_A* 1qn6_A* 1qn7_A* 1qn8_A* 1qn9_A* 1qn4_A* 1qnb_A* 1qnc_A* 1qne_A* 1vok_A 1vol_B* 1vto_A* 1vtl_E* ...

Probab=100.00  E-value=8.7e-59  Score=371.23  Aligned_cols=155  Identities=80%  Similarity=1.259  Sum_probs=151.7

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      +++.|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++++.|+++++
T Consensus         1 ~~~~~~I~NiVas~~l~~~ldL~~ia~~~~n~eYePe~fpgli~R~~~Pk~~~lIF~SGKiv~TGaks~e~~~~a~~~i~   80 (180)
T 1ytb_A            1 SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYA   80 (180)
T ss_dssp             CCCCCEEEEEEEEEECCSCCCHHHHHHHSSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCceEEEEEEEEEEcCCccCHHHHHhhCCCCEECccccCCEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHH
Confidence            3689999999999999999999999999999999999                        9999999999999999999


Q ss_pred             HHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013           66 RIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR  145 (167)
Q Consensus        66 ~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~  145 (167)
                      ++|+++|+++++.+|+|||||||+|++++|||+++|..++++++||||+||||+||+.+|+++++||+||||+|||||++
T Consensus        81 ~~L~~lg~~~~~~~~~i~NIvas~dl~~~I~Le~la~~~~~~~~YEPE~fPGliyR~~~pkv~~lIF~SGkivitGak~~  160 (180)
T 1ytb_A           81 RIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQR  160 (180)
T ss_dssp             HHHHHHTCCCCCEEEEEEEEEEEEECSSCBCHHHHHHHTTTTEECCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSH
T ss_pred             HHHHHcCCCcccccceEEEEEEEEECCCccCHHHHHHhcccceEECCccCCcEEEEeCCCcEEEEEecCCeEEEEecCCH
Confidence            99999999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhh
Q 031013          146 DETYTAFENIYPVLTEFRK  164 (167)
Q Consensus       146 e~~~~a~~~i~~~L~~~r~  164 (167)
                      +|+++|++.|+|+|.+||+
T Consensus       161 ~~~~~a~~~i~p~L~~~~~  179 (180)
T 1ytb_A          161 EEIYQAFEAIYPVLSEFRK  179 (180)
T ss_dssp             HHHHHHHHHHHHHHHHTBC
T ss_pred             HHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999997

>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C

Probab=100.00  E-value=1.8e-58  Score=378.27  Aligned_cols=156  Identities=72%  Similarity=1.180  Sum_probs=151.9

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      +|+.|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++++.|+++++
T Consensus        39 ~~i~~~I~NIVas~~l~~~ldL~~ia~~~~n~eYePe~Fpglv~Rl~~Pk~t~LIF~SGKiV~TGAkS~e~a~~A~~ki~  118 (218)
T 3eik_A           39 SGIIPTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGAKSEKSSRMAAQRYA  118 (218)
T ss_dssp             -CCSCEEEEEEEEEECSSCCCHHHHHHHCTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCceEEEEEEEEEECCCccCHHHHHhhCCCcEEcCccCceEEEEecCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999                        9999999999999999999


Q ss_pred             HHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013           66 RIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR  145 (167)
Q Consensus        66 ~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~  145 (167)
                      ++|+++|+++++.+|+|+|||||||++|+|||++||..++.+++||||+||||+||+.+|+++++||+||||+|||||++
T Consensus       119 ~~L~~lG~~v~~~~fkIqNIvas~dl~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~pkvt~lIF~SGKiviTGaks~  198 (218)
T 3eik_A          119 KIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSNYCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVR  198 (218)
T ss_dssp             HHHHHTTCCCCCEEEEEEEEEEEEECSSCBCHHHHHHHSTTTEECCTTTSSSEEEEETTTTEEEEECTTSEEEEEEESSH
T ss_pred             HHHHHcCCCcccccceEEEEEEEEECCCcCcHHHHHHhccCCcEECCccCceEEEEcCCCCEEEEEeCCCeEEEEecCCH
Confidence            99999999999999999999999999999999999998888999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhhh
Q 031013          146 DETYTAFENIYPVLTEFRKV  165 (167)
Q Consensus       146 e~~~~a~~~i~~~L~~~r~~  165 (167)
                      +|+++|++.|+|+|.+|||.
T Consensus       199 ~d~~~A~~~I~p~L~~frk~  218 (218)
T 3eik_A          199 DDIYQAFNNIYPVLIQHRKA  218 (218)
T ss_dssp             HHHHHHHHHHHHHHHHTBC-
T ss_pred             HHHHHHHHHHHHHHHHhhcC
Confidence            99999999999999999984

>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein, transcription factor, transcription regulation; 1.90A {Methanococcus jannaschii}

Probab=100.00  E-value=1.6e-56  Score=360.32  Aligned_cols=152  Identities=36%  Similarity=0.643  Sum_probs=143.3

Q ss_pred             CeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHH
Q 031013           12 AVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARI   67 (167)
Q Consensus        12 ~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~   67 (167)
                      ..|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++++.|+++++++
T Consensus        11 ~~~~i~NvVas~~l~~~ldL~~ia~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~TGAkS~e~a~~a~~~~~~~   90 (188)
T 2z8u_A           11 PEIKIVNVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKSKEEAEIAIKKIIKE   90 (188)
T ss_dssp             CCCEEEEEEEEEECCSSCCHHHHHHHSSCCC-------CEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEEEeCCeeCHHHHHhhCCCCEECCCCcccEEEEcCCCcEEEEEeCCCeEEEecCCCHHHHHHHHHHHHHH
Confidence            36899999999999999999999999999999999                        999999999999999999999


Q ss_pred             HHhcCCC-CcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHH
Q 031013           68 IQKLGFP-AKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRD  146 (167)
Q Consensus        68 l~~lg~~-~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e  146 (167)
                      |+++|++ .++.+|+|+|||||+|++++|||++|+..+ ++++||||+||||+||+.+|+++++||+||||+||||||++
T Consensus        91 L~~lg~~~~~~~~~~I~NIVas~~l~~~i~L~~la~~~-~~~eYePe~fPgliyR~~~Pk~t~lIF~SGKiviTGaks~~  169 (188)
T 2z8u_A           91 LKDAGIDVIENPEIKIQNMVATADLGIEPNLDDIALMV-EGTEYEPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEE  169 (188)
T ss_dssp             HHHTTCCCCSSCCCEEEEEEEEEECSSCCCHHHHHHHS-TTEEECTTTSSSEEEEEETTEEEEEECTTSEEEEESCSCHH
T ss_pred             HHhcCCCccccCceEEEEEEEEEecCCccCHHHHHhhC-cCcEECCccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHH
Confidence            9999998 688999999999999999999999999986 69999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhh
Q 031013          147 ETYTAFENIYPVLTEFRK  164 (167)
Q Consensus       147 ~~~~a~~~i~~~L~~~r~  164 (167)
                      |+++|+++++|+|+++++
T Consensus       170 ~~~~A~~~i~~~L~~~~~  187 (188)
T 2z8u_A          170 DAKRALKKILDTIKEVQE  187 (188)
T ss_dssp             HHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHhcc
Confidence            999999999999999986

>1rm1_A Tata-box binding protein; yeast TFIIA, TBP protein, ATA-box DNA, transcription/DNA complex; 2.50A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1

Probab=100.00  E-value=2.4e-56  Score=370.51  Aligned_cols=156  Identities=79%  Similarity=1.254  Sum_probs=152.1

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      .++.|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++++.|+++++
T Consensus        61 ~~~~~~I~NIVas~~l~~~ldL~~ia~~~~n~eYePe~Fpgli~Rl~~Pk~t~lIF~SGKiV~TGaks~e~a~~A~~~i~  140 (240)
T 1rm1_A           61 SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYA  140 (240)
T ss_dssp             CCCCCEEEEEEEEEECCSCCCHHHHHHHBTTEEECTTTCSEEEEEEETTEEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCceEEEEEEEEEEcCCccCHHHHHhhCCCcEEcCcccceEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHH
Confidence            3678999999999999999999999999999999999                        9999999999999999999


Q ss_pred             HHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013           66 RIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR  145 (167)
Q Consensus        66 ~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~  145 (167)
                      ++|+++|+++++.+|+|||||||||++|+|||++|+..++++++||||+||||+||+.+|+++++||+||||+|||+|++
T Consensus       141 ~~L~~lg~~~~~~~f~IqNIVas~dl~f~I~Le~la~~~~~~~~YEPE~fPGLiyR~~~pkvvllIF~SGKIviTGaK~~  220 (240)
T 1rm1_A          141 RIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQR  220 (240)
T ss_dssp             HHHHHHTCCCCCEEEEEEEEEEEEECSSCBCHHHHHHHTTTTEEEETTTEEEEEEEETTTTEEEEECTTSEEEEEEESSH
T ss_pred             HHHHHcCCCcccCcceEEEEEEEEeCCCccCHHHHHHhchhccEECCccCCceEEEeCCCcEEEEEecCCEEEEEecCCH
Confidence            99999999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhhh
Q 031013          146 DETYTAFENIYPVLTEFRKV  165 (167)
Q Consensus       146 e~~~~a~~~i~~~L~~~r~~  165 (167)
                      +|+++|++.|+|+|.+||+.
T Consensus       221 ~~~~~Ai~~i~p~L~~~~~~  240 (240)
T 1rm1_A          221 EEIYQAFEAIYPVLSEFRKM  240 (240)
T ss_dssp             HHHHHHHHHHHHHHHHTBCC
T ss_pred             HHHHHHHHHHHHHHHHhccC
Confidence            99999999999999999974

>1mp9_A Tata-binding protein; transcription regulation, DNA-binding protein, transcription factor, DNA binding protein; 2.00A {Sulfolobus acidocaldarius} SCOP: d.129.1.1 d.129.1.1

Probab=100.00  E-value=1.3e-55  Score=357.40  Aligned_cols=155  Identities=43%  Similarity=0.658  Sum_probs=150.0

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      .++.|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++++.|+++++
T Consensus         9 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~TGakS~e~a~~a~~~i~   88 (198)
T 1mp9_A            9 YKAVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRII   88 (198)
T ss_dssp             CCCEEEEEEEEEEEECCSCCCHHHHHHHSTTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHH
T ss_pred             CCCceEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccccceEEEcCCCceEEEEeCCCeEEEeccCCHHHHHHHHHHHH
Confidence            3678999999999999999999999999999999999                        9999999999999999999


Q ss_pred             HHHHhcCCC-CcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCC
Q 031013           66 RIIQKLGFP-AKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKV  144 (167)
Q Consensus        66 ~~l~~lg~~-~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks  144 (167)
                      ++|+++|++ .++.+|+|+|||||++++++|||++++..+ ++++||||+||||+||+.+|+++++||+||||+||||||
T Consensus        89 ~~L~~lG~~~~~~~~~~I~NIVas~~l~~~i~L~~la~~~-~~~~YePe~fPgliyR~~~Pk~t~lIF~SGKiviTGaks  167 (198)
T 1mp9_A           89 KTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLL-ENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKR  167 (198)
T ss_dssp             HHHHHTTCCCSSCCEEEEEEEEEEEECSSEECHHHHHHHS-SSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESS
T ss_pred             HHHHHcCCcccCcCceEEEEEEEEeeCCCccCHHHHHhhc-CCcEECCccCCeEEEEeCCCcEEEEEeCCCEEEEEecCC
Confidence            999999998 688999999999999999999999999986 699999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhhhh
Q 031013          145 RDETYTAFENIYPVLTEFRKV  165 (167)
Q Consensus       145 ~e~~~~a~~~i~~~L~~~r~~  165 (167)
                      ++++++|+++++|+|++++..
T Consensus       168 ~~~~~~A~~~i~~~L~~~~~~  188 (198)
T 1mp9_A          168 EDEVHKAVKKIFDKLVELDCV  188 (198)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHHHHHHhCCC
Confidence            999999999999999999864

>1ais_A TBP, protein (tata-binding protein); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: d.129.1.1 d.129.1.1 PDB: 1d3u_A* 1pcz_A

Probab=100.00  E-value=1.6e-55  Score=352.77  Aligned_cols=151  Identities=38%  Similarity=0.592  Sum_probs=146.7

Q ss_pred             CCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHH
Q 031013           11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYAR   66 (167)
Q Consensus        11 ~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~   66 (167)
                      ...|+|+|||||++++|+|||++||..++|+||||+                        +||||+|+++++.|++++++
T Consensus         6 ~~~~~I~NvVas~~l~~~ldL~~ia~~~~n~eY~P~~fpgli~Rl~~P~~t~lIF~SGKiv~TGakS~~~~~~a~~~i~~   85 (182)
T 1ais_A            6 KVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQ   85 (182)
T ss_dssp             TCEEEEEEEEEEEECCSCCCHHHHTTTSTTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCceEEEEEEEEEEcCCeeCHHHHHhhCCCcEECCCccccEEEEcCCCcEEEEEeCCCeEEEecCCCHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999999                        99999999999999999999


Q ss_pred             HHHhcCCC-CcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013           67 IIQKLGFP-AKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR  145 (167)
Q Consensus        67 ~l~~lg~~-~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~  145 (167)
                      +|+++|++ .++.+|+|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+++++||+||||+||||||+
T Consensus        86 ~L~~lG~~~~~~~~~~I~NIVas~~l~~~i~L~~la~~~-~~~~YePe~fpgli~R~~~pk~~~lIF~SGKiviTGaks~  164 (182)
T 1ais_A           86 KLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTL-PNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSE  164 (182)
T ss_dssp             HHHHTTCCCSSSCEEEEEEEEEEEECSSCCCHHHHHHHS-TTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSH
T ss_pred             HHHHcCCCcccccceEEEEEEEEEEcCCccCHHHHHhhC-CCCEECCccCceEEEEeCCCcEEEEEecCCEEEEEecCCH
Confidence            99999998 688999999999999999999999999987 6999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhh
Q 031013          146 DETYTAFENIYPVLTEF  162 (167)
Q Consensus       146 e~~~~a~~~i~~~L~~~  162 (167)
                      +|+++|+++++|+|+++
T Consensus       165 ~~~~~a~~~i~~~L~~~  181 (182)
T 1ais_A          165 ADAWEAVRKLLRELDKY  181 (182)
T ss_dssp             HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999999875

>1rm1_A Tata-box binding protein; yeast TFIIA, TBP protein, ATA-box DNA, transcription/DNA complex; 2.50A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1

Probab=100.00  E-value=1.7e-33  Score=233.45  Aligned_cols=116  Identities=27%  Similarity=0.334  Sum_probs=84.0

Q ss_pred             ceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCe
Q 031013           47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPK  126 (167)
Q Consensus        47 v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk  126 (167)
                      .-.|+.|.+++..+++++++.++++|++....+++|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+
T Consensus        32 sGk~~~s~~~s~~~~~~~~~~~~~~~~~~~~~~~~I~NIVas~~l~~~ldL~~ia~~~-~n~eYePe~Fpgli~Rl~~Pk  110 (240)
T 1rm1_A           32 DGTKPATTFQSEEDIKRAAPESEKDTSATSGIVPTLQNIVATVTLGCRLDLKTVALHA-RNAEYNPKRFAAVIMRIREPK  110 (240)
T ss_dssp             -----------------------------CCCCCEEEEEEEEEECCSCCCHHHHHHHB-TTEEECTTTCSEEEEEEETTE
T ss_pred             CCcceecccccHHHHHHHHHHHHhhccCcCCCceEEEEEEEEEEcCCccCHHHHHhhC-CCcEEcCcccceEEEEeCCCc
Confidence            3446677777777788888999999998777789999999999999999999999987 689999999999999999999


Q ss_pred             EEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHhhh
Q 031013          127 IVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFR  163 (167)
Q Consensus       127 ~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~r  163 (167)
                      ++++||+||||+||||||+++++.|+++++++|+++.
T Consensus       111 ~t~lIF~SGKiV~TGaks~e~a~~A~~~i~~~L~~lg  147 (240)
T 1rm1_A          111 TTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIG  147 (240)
T ss_dssp             EEEEEETTSEEEEEEESSHHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999999999999875

>1ytb_A Protein (tata binding protein (TBP)); protein-DNA complex, transcription/DNA complex; HET: DNA; 1.80A {Saccharomyces cerevisiae} SCOP: d.129.1.1 d.129.1.1 PDB: 1ngm_A* 1tba_B 1nh2_A* 1ytf_A* 1tbp_A 1qna_A* 1qn3_A* 1qn5_A* 1qn6_A* 1qn7_A* 1qn8_A* 1qn9_A* 1qn4_A* 1qnb_A* 1qnc_A* 1qne_A* 1vok_A 1vol_B* 1vto_A* 1vtl_E* ...

Probab=99.96  E-value=5.9e-30  Score=204.38  Aligned_cols=84  Identities=31%  Similarity=0.507  Sum_probs=81.0

Q ss_pred             ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013           79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV  158 (167)
Q Consensus        79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~  158 (167)
                      .++|+|||||++++++|||+++|..+ ++++||||+||||+||+.+|+++++||+||||+||||||+++++.|+++++++
T Consensus         4 ~~~I~NiVas~~l~~~ldL~~ia~~~-~n~eYePe~fpgli~R~~~Pk~~~lIF~SGKiv~TGaks~e~~~~a~~~i~~~   82 (180)
T 1ytb_A            4 VPTLQNIVATVTLGCRLDLKTVALHA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARI   82 (180)
T ss_dssp             CCEEEEEEEEEECCSCCCHHHHHHHS-SSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEEcCCccCHHHHHhhC-CCCEECccccCCEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            57999999999999999999999887 68999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhh
Q 031013          159 LTEFR  163 (167)
Q Consensus       159 L~~~r  163 (167)
                      |+++-
T Consensus        83 L~~lg   87 (180)
T 1ytb_A           83 IQKIG   87 (180)
T ss_dssp             HHHHT
T ss_pred             HHHcC
Confidence            99874

>1ais_A TBP, protein (tata-binding protein); hyperthermophIle, ribosome binding, complex (ribosome binding/ DNA); HET: DNA 5IU; 2.10A {Pyrococcus woesei} SCOP: d.129.1.1 d.129.1.1 PDB: 1d3u_A* 1pcz_A

Probab=99.95  E-value=3.9e-28  Score=194.07  Aligned_cols=85  Identities=38%  Similarity=0.570  Sum_probs=81.4

Q ss_pred             ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013           77 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY  156 (167)
Q Consensus        77 ~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~  156 (167)
                      ..+++|+|||||++++++|||+++|..+ ++++||||+|||++||+.+|+++++||+||||+||||||+++++.|++++.
T Consensus         6 ~~~~~I~NvVas~~l~~~ldL~~ia~~~-~n~eY~P~~fpgli~Rl~~P~~t~lIF~SGKiv~TGakS~~~~~~a~~~i~   84 (182)
T 1ais_A            6 KVKLRIENIVASVDLFAQLDLEKVLDLC-PNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLA   84 (182)
T ss_dssp             TCEEEEEEEEEEEECCSCCCHHHHTTTS-TTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCceEEEEEEEEEEcCCeeCHHHHHhhC-CCcEECCCccccEEEEcCCCcEEEEEeCCCeEEEecCCCHHHHHHHHHHHH
Confidence            4578999999999999999999999987 599999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhh
Q 031013          157 PVLTEF  162 (167)
Q Consensus       157 ~~L~~~  162 (167)
                      ++|+++
T Consensus        85 ~~L~~l   90 (182)
T 1ais_A           85 QKLKSI   90 (182)
T ss_dssp             HHHHHT
T ss_pred             HHHHHc
Confidence            999875

>3eik_A Tata-box-binding protein; DNA-binding, initiation factor, nucleus, transcription; 1.90A {Encephalitozoon cuniculi} PDB: 3oci_A 3oc3_C

Probab=99.95  E-value=5.6e-28  Score=197.77  Aligned_cols=83  Identities=30%  Similarity=0.525  Sum_probs=80.2

Q ss_pred             ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013           79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV  158 (167)
Q Consensus        79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~  158 (167)
                      .++|+|||||++++++|||+++|..+ ++++||||+||||+||+.+|+++++||+||||+||||||+++++.|++++..+
T Consensus        42 ~~~I~NIVas~~l~~~ldL~~ia~~~-~n~eYePe~Fpglv~Rl~~Pk~t~LIF~SGKiV~TGAkS~e~a~~A~~ki~~~  120 (218)
T 3eik_A           42 IPTLQNVVATVNLSCKLDLKNIALRA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGAKSEKSSRMAAQRYAKI  120 (218)
T ss_dssp             SCEEEEEEEEEECSSCCCHHHHHHHC-TTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEECCCccCHHHHHhhC-CCcEEcCccCceEEEEecCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            57899999999999999999999987 69999999999999999999999999999999999999999999999999999


Q ss_pred             HHhh
Q 031013          159 LTEF  162 (167)
Q Consensus       159 L~~~  162 (167)
                      |+++
T Consensus       121 L~~l  124 (218)
T 3eik_A          121 IHKL  124 (218)
T ss_dssp             HHHT
T ss_pred             HHHc
Confidence            9875

>1mp9_A Tata-binding protein; transcription regulation, DNA-binding protein, transcription factor, DNA binding protein; 2.00A {Sulfolobus acidocaldarius} SCOP: d.129.1.1 d.129.1.1

Probab=99.95  E-value=1.5e-27  Score=192.90  Aligned_cols=85  Identities=39%  Similarity=0.633  Sum_probs=81.7

Q ss_pred             ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013           77 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY  156 (167)
Q Consensus        77 ~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~  156 (167)
                      ..+++|+|||||++++++|||++||..+ ++++|||++|||++||+.+|+++++||+||||+||||||+++++.|++++.
T Consensus        10 ~~~~~I~NvVas~~l~~~ldL~~la~~~-~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~TGakS~e~a~~a~~~i~   88 (198)
T 1mp9_A           10 KAVVNIENIVATVTLDQTLDLYAMERSV-PNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRII   88 (198)
T ss_dssp             CCEEEEEEEEEEEECCSCCCHHHHHHHS-TTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHH
T ss_pred             CCceEEEEEEEEEEcCCcccHHHHHhhC-CCCEECCccccceEEEcCCCceEEEEeCCCeEEEeccCCHHHHHHHHHHHH
Confidence            4579999999999999999999999988 599999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhh
Q 031013          157 PVLTEF  162 (167)
Q Consensus       157 ~~L~~~  162 (167)
                      ++|+++
T Consensus        89 ~~L~~l   94 (198)
T 1mp9_A           89 KTLKKY   94 (198)
T ss_dssp             HHHHHT
T ss_pred             HHHHHc
Confidence            999875

>2z8u_A Tata-box-binding protein; transcription, DNA-binding protein, transcription factor, transcription regulation; 1.90A {Methanococcus jannaschii}

Probab=99.95  E-value=1.5e-27  Score=191.57  Aligned_cols=85  Identities=41%  Similarity=0.581  Sum_probs=74.3

Q ss_pred             ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013           77 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY  156 (167)
Q Consensus        77 ~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~  156 (167)
                      ..+++|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||||+++++.|.+++.
T Consensus        10 ~~~~~i~NvVas~~l~~~ldL~~ia~~~-~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~TGAkS~e~a~~a~~~~~   88 (188)
T 2z8u_A           10 EPEIKIVNVVVSTKIGDNIDLEEVAMIL-ENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKSKEEAEIAIKKII   88 (188)
T ss_dssp             -CCCEEEEEEEEEECCSSCCHHHHHHHS-SCCC-------CEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEEEEEEeCCeeCHHHHHhhC-CCCEECCCCcccEEEEcCCCcEEEEEeCCCeEEEecCCCHHHHHHHHHHHH
Confidence            3578999999999999999999999988 599999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhh
Q 031013          157 PVLTEF  162 (167)
Q Consensus       157 ~~L~~~  162 (167)
                      ++|+++
T Consensus        89 ~~L~~l   94 (188)
T 2z8u_A           89 KELKDA   94 (188)
T ss_dssp             HHHHHT
T ss_pred             HHHHhc
Confidence            999886

>3vn5_A RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {Aquifex aeolicus}

Probab=93.82  E-value=0.025  Score=46.80  Aligned_cols=39  Identities=10%  Similarity=0.217  Sum_probs=33.0

Q ss_pred             cCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHH
Q 031013          112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYT  150 (167)
Q Consensus       112 PE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~  150 (167)
                      +..=|+..|+...+.+++.+|.|||+++.|...++.+..
T Consensus        25 ~~~~~~~~f~~k~~~~~it~Y~SGkv~fqG~~a~~~a~~   63 (257)
T 3vn5_A           25 KINAPYTLWALEGNGVKVYYYKTGSLLIQGKNSEKVLKE   63 (257)
T ss_dssp             ECCCTTCSEEEEETTEEEEECTTSEEEEESTTHHHHHHH
T ss_pred             ccCCCceEEEEecCCeEEEEEeccEEEEeCCCHHHHHHH
Confidence            455689999999999999999999999999877654443

>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A 3asm_A

Probab=93.65  E-value=0.065  Score=45.32  Aligned_cols=36  Identities=28%  Similarity=0.626  Sum_probs=31.6

Q ss_pred             CCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013          113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET  148 (167)
Q Consensus       113 E~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~  148 (167)
                      ..-|+..|+...+.+++.+|.|||+++.|...++.+
T Consensus        27 ~~~~~~~f~~k~~~~~it~Y~SGkv~~qG~~a~~~~   62 (310)
T 2d0b_A           27 RLPAGALFAVKRPDVVITAYRSGKVLFQGKAAEQEA   62 (310)
T ss_dssp             SCCTTEEEEECCTTCEEEEETTSEEEEESTTHHHHH
T ss_pred             CCCCCeEEEecCCCeEEEEEeCCEEEEeCCchHHHH
Confidence            446899999999999999999999999998876443

>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=81.72  E-value=2.5  Score=29.75  Aligned_cols=41  Identities=17%  Similarity=0.297  Sum_probs=32.7

Q ss_pred             CCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHhhhhh
Q 031013          115 FPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV  165 (167)
Q Consensus       115 fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~r~~  165 (167)
                      ||++...+.+        .++.|+|+|.  .+++..|...|..++.+++..
T Consensus        56 ~~~v~I~fp~--------~~~~ItI~G~--~~~V~~a~~~I~~~v~el~~~   96 (102)
T 2ctf_A           56 MPKVHIEFTE--------GEDKITLEGP--TEDVSVAQEQIEGMVKDLINR   96 (102)
T ss_dssp             CSSSEEEECS--------SSCEEEEEEC--HHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCcEEEeCC--------CCCEEEEECC--HHHHHHHHHHHHHHHHHHHhh
Confidence            5666555544        5889999999  678999999999999988764

---

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	167
d1qnaa2	83	d.129.1.1 (A:116-198) TATA-box binding protein (TB	5e-39
d1qnaa2	83	d.129.1.1 (A:116-198) TATA-box binding protein (TB	4e-08
d1mp9a2	101	d.129.1.1 (A:97-197) TATA-box binding protein (TBP	1e-36
d1mp9a2	101	d.129.1.1 (A:97-197) TATA-box binding protein (TBP	4e-15
d1aisa2	89	d.129.1.1 (A:93-181) TATA-box binding protein (TBP	1e-34
d1aisa2	89	d.129.1.1 (A:93-181) TATA-box binding protein (TBP	4e-14
d1aisa1	92	d.129.1.1 (A:1-92) TATA-box binding protein (TBP),	1e-34
d1aisa1	92	d.129.1.1 (A:1-92) TATA-box binding protein (TBP),	4e-16
d1mp9a1	92	d.129.1.1 (A:5-96) TATA-box binding protein (TBP),	3e-32
d1mp9a1	92	d.129.1.1 (A:5-96) TATA-box binding protein (TBP),	2e-16
d1qnaa1	99	d.129.1.1 (A:17-115) TATA-box binding protein (TBP	2e-31
d1qnaa1	99	d.129.1.1 (A:17-115) TATA-box binding protein (TBP	3e-24

>d1qnaa2 d.129.1.1 (A:116-198) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 83

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  125 bits (316), Expect = 5e-39
 Identities = 77/83 (92%), Positives = 80/83 (96%)

Query: 83  QNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGA 142
           QNIVGSCDVKFPIRLEGLAYSH AFSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGA
Sbjct: 1   QNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGA 60

Query: 143 KVRDETYTAFENIYPVLTEFRKV 165
           K+RDETY AFENIYPVL+EFRK+
Sbjct: 61  KMRDETYKAFENIYPVLSEFRKI 83

>d1qnaa2 d.129.1.1 (A:116-198) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 83

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 46.3 bits (110), Expect = 4e-08
 Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 25/79 (31%)

Query: 18 NIVSTVNLDCKLDLKKIALQAR-NAEYNPK------------------------VCTGAK 52
          NIV + ++   + L+ +A      + Y P+                        V TGAK
Sbjct: 2  NIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAK 61

Query: 53 SEQQSKLAARKYARIIQKL 71
             ++  A      ++ + 
Sbjct: 62 MRDETYKAFENIYPVLSEF 80

>d1mp9a2 d.129.1.1 (A:97-197) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 101

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score =  120 bits (302), Expect = 1e-36
 Identities = 42/88 (47%), Positives = 57/88 (64%), Gaps = 1/88 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
             +IQNIV S ++   + L+  A+     + YEPE FPGLIYRM +P++VLLIF SGK+V
Sbjct: 7   KIQIQNIVASANLHVIVNLDKAAF-LLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMV 65

Query: 139 ITGAKVRDETYTAFENIYPVLTEFRKVQ 166
           ITGAK  DE + A + I+  L E   V+
Sbjct: 66  ITGAKREDEVHKAVKKIFDKLVELDCVK 93

>d1mp9a2 d.129.1.1 (A:97-197) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 101

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score = 65.2 bits (159), Expect = 4e-15
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 26/92 (28%)

Query: 16  VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
           ++NIV++ NL   ++L K A    N  Y P+                        V TGA
Sbjct: 10  IQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGA 69

Query: 52  KSEQQSKLAARKYARIIQKLGF--PAKFKDFK 81
           K E +   A +K    + +L    P + ++ +
Sbjct: 70  KREDEVHKAVKKIFDKLVELDCVKPVEEEELE 101

>d1aisa2 d.129.1.1 (A:93-181) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 89

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score =  114 bits (288), Expect = 1e-34
 Identities = 36/90 (40%), Positives = 53/90 (58%), Gaps = 4/90 (4%)

Query: 76  KFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIF 132
           KFK      +QN+V S D+     L+ +A +      YEPE FPG+IYR+K+PK V+L+F
Sbjct: 1   KFKRAPQIDVQNMVFSGDIGREFNLDVVALTLP-NCEYEPEQFPGVIYRVKEPKSVILLF 59

Query: 133 VSGKIVITGAKVRDETYTAFENIYPVLTEF 162
            SGKIV +GAK   + + A   +   L ++
Sbjct: 60  SSGKIVCSGAKSEADAWEAVRKLLRELDKY 89

>d1aisa2 d.129.1.1 (A:93-181) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 89

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 62.1 bits (151), Expect = 4e-14
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 24/79 (30%)

Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
          V+N+V + ++  + +L  +AL   N EY P+                        VC+GA
Sbjct: 10 VQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGA 69

Query: 52 KSEQQSKLAARKYARIIQK 70
          KSE  +  A RK  R + K
Sbjct: 70 KSEADAWEAVRKLLRELDK 88

>d1aisa1 d.129.1.1 (A:1-92) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 92

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score =  114 bits (288), Expect = 1e-34
 Identities = 32/83 (38%), Positives = 44/83 (53%), Gaps = 1/83 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
             +I+NIV S D+   + LE +       S Y PE FPG+I  +  PK+ LLIF SGK+V
Sbjct: 8   KLRIENIVASVDLFAQLDLEKVLD-LCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLV 66

Query: 139 ITGAKVRDETYTAFENIYPVLTE 161
           +TGAK   +   A   +   L  
Sbjct: 67  VTGAKSVQDIERAVAKLAQKLKS 89

>d1aisa1 d.129.1.1 (A:1-92) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Length = 92

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

 Score = 67.4 bits (165), Expect = 4e-16
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 24/81 (29%)

Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
          ++NIV++V+L  +LDL+K+     N++YNP+                        V TGA
Sbjct: 11 IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70

Query: 52 KSEQQSKLAARKYARIIQKLG 72
          KS Q  + A  K A+ ++ +G
Sbjct: 71 KSVQDIERAVAKLAQKLKSIG 91

>d1mp9a1 d.129.1.1 (A:5-96) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 92

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score =  108 bits (272), Expect = 3e-32
 Identities = 32/84 (38%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 79  DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIV 138
              I+NIV +  +   + L  +         Y+P+ FPGLI+R++ PKI  LIF SGK+V
Sbjct: 8   VVNIENIVATVTLDQTLDLYAME-RSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMV 66

Query: 139 ITGAKVRDETYTAFENIYPVLTEF 162
           +TGAK  DE   A + I   L ++
Sbjct: 67  VTGAKSTDELIKAVKRIIKTLKKY 90

>d1mp9a1 d.129.1.1 (A:5-96) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 92

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score = 68.2 bits (167), Expect = 2e-16
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 24/81 (29%)

Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
          ++NIV+TV LD  LDL  +     N EY+P                         V TGA
Sbjct: 11 IENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGA 70

Query: 52 KSEQQSKLAARKYARIIQKLG 72
          KS  +   A ++  + ++K G
Sbjct: 71 KSTDELIKAVKRIIKTLKKYG 91

>d1qnaa1 d.129.1.1 (A:17-115) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 99

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  106 bits (267), Expect = 2e-31
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 81  KIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVIT 140
            +QNIV + ++   + L+ +A      + Y P+ F  +I R+++PK   LIF SGK+V T
Sbjct: 8   TLQNIVSTVNLDCKLDLKAIA-LQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCT 66

Query: 141 GAKVRDETYTAFENIYPVLTE 161
           GAK  D +  A      ++ +
Sbjct: 67  GAKSEDFSKMAARKYARIVQK 87

>d1qnaa1 d.129.1.1 (A:17-115) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 99

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 88.3 bits (219), Expect = 3e-24
 Identities = 62/96 (64%), Positives = 67/96 (69%), Gaps = 24/96 (25%)

Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
          G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK                        
Sbjct: 4  GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 63

Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKI 82
          VCTGAKSE  SK+AARKYARI+QKLGFPAKFKDFKI
Sbjct: 64 VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKI 99

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	167
d1qnaa2	83	TATA-box binding protein (TBP), C-terminal domain	100.0
d1aisa2	89	TATA-box binding protein (TBP), C-terminal domain	100.0
d1mp9a2	101	TATA-box binding protein (TBP), C-terminal domain	100.0
d1aisa1	92	TATA-box binding protein (TBP), C-terminal domain	100.0
d1mp9a1	92	TATA-box binding protein (TBP), C-terminal domain	100.0
d1qnaa1	99	TATA-box binding protein (TBP), C-terminal domain	100.0
d1qnaa1	99	TATA-box binding protein (TBP), C-terminal domain	99.9
d1mp9a1	92	TATA-box binding protein (TBP), C-terminal domain	99.76
d1aisa1	92	TATA-box binding protein (TBP), C-terminal domain	99.75
d1aisa2	89	TATA-box binding protein (TBP), C-terminal domain	99.71
d1mp9a2	101	TATA-box binding protein (TBP), C-terminal domain	99.67
d1qnaa2	83	TATA-box binding protein (TBP), C-terminal domain	99.54

>d1qnaa2 d.129.1.1 (A:116-198) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=100.00  E-value=8.2e-36  Score=209.61  Aligned_cols=82  Identities=94%  Similarity=1.466  Sum_probs=80.4

Q ss_pred             EEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHhh
Q 031013           83 QNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF  162 (167)
Q Consensus        83 ~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~  162 (167)
                      ||||||++++++|||++||..++.+++||||+||||+||+.+|+++++||+||||+||||||++|+++|+++|+|+|++|
T Consensus         1 qNiVas~~l~~~I~L~~la~~~~~~~~YePe~fpgl~~R~~~pk~~~lIF~SGkivitGaks~~~~~~a~~~i~~~L~~~   80 (83)
T d1qnaa2           1 QNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEF   80 (83)
T ss_dssp             EEEEEEEECSSCBCHHHHHHHTTTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCccHHHHHHhhhhhcccChhhCCeEEEEECCCCeEEEEEcCCEEEEECCCCHHHHHHHHHHHHHHHHHh
Confidence            79999999999999999999887789999999999999999999999999999999999999999999999999999999


Q ss_pred             hh
Q 031013          163 RK  164 (167)
Q Consensus       163 r~  164 (167)
                      ||
T Consensus        81 ~k   82 (83)
T d1qnaa2          81 RK   82 (83)
T ss_dssp             BC
T ss_pred             cc
Confidence            97

>d1aisa2 d.129.1.1 (A:93-181) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=100.00  E-value=1.1e-34  Score=206.35  Aligned_cols=84  Identities=39%  Similarity=0.670  Sum_probs=81.3

Q ss_pred             cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013           78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP  157 (167)
Q Consensus        78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~  157 (167)
                      ++++|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+++++||+||||+||||||++|+++|+++++|
T Consensus         6 p~i~I~NiVas~~l~~~idL~~la~~~-~~~~Y~Pe~fpgli~R~~~p~~t~lIF~SGKivitGaks~~~~~~a~~~i~~   84 (89)
T d1aisa2           6 PQIDVQNMVFSGDIGREFNLDVVALTL-PNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLR   84 (89)
T ss_dssp             CEEEEEEEEEEEECSSCCCHHHHHHHS-TTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEEEEECCCcccHHHHHhhc-cCcEECcccCceEEEEEcCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHH
Confidence            479999999999999999999999988 5999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q 031013          158 VLTEF  162 (167)
Q Consensus       158 ~L~~~  162 (167)
                      +|++|
T Consensus        85 ~L~k~   89 (89)
T d1aisa2          85 ELDKY   89 (89)
T ss_dssp             HHTTC
T ss_pred             HHhcC
Confidence            99886

>d1mp9a2 d.129.1.1 (A:97-197) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=100.00  E-value=9.9e-34  Score=205.60  Aligned_cols=87  Identities=47%  Similarity=0.739  Sum_probs=83.8

Q ss_pred             ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013           77 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY  156 (167)
Q Consensus        77 ~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~  156 (167)
                      ..+++|+|||||++++++|||++||..+ ++++||||+||||+||+.+|+++++||+||||+||||||++++++|+++++
T Consensus         5 ~p~~~v~NiVas~~l~~~idL~~la~~~-~~~~YePe~fpgli~R~~~pk~t~lIF~SGKivitGaks~~~~~~a~~~i~   83 (101)
T d1mp9a2           5 KPKIQIQNIVASANLHVIVNLDKAAFLL-ENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIF   83 (101)
T ss_dssp             CCEEEEEEEEEEEECSSEECHHHHHHHS-SSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEEEECCCcccHHHHHhhC-CCCEECcccCCeEEEEecCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHH
Confidence            3489999999999999999999999988 589999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhh
Q 031013          157 PVLTEFRK  164 (167)
Q Consensus       157 ~~L~~~r~  164 (167)
                      |+|.+++.
T Consensus        84 ~~L~~~~~   91 (101)
T d1mp9a2          84 DKLVELDC   91 (101)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHhCC
Confidence            99999985

>d1aisa1 d.129.1.1 (A:1-92) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=100.00  E-value=8.8e-34  Score=202.68  Aligned_cols=88  Identities=36%  Similarity=0.546  Sum_probs=83.0

Q ss_pred             CCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHH
Q 031013           74 PAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFE  153 (167)
Q Consensus        74 ~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~  153 (167)
                      +....+++|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+++++||+|||++||||||++++++|++
T Consensus         3 d~~~~~~~I~NiVas~~l~~~idL~~la~~~-~~~~YePe~fpgl~~R~~~p~~~~lIF~sGkivitGakS~~~~~~a~~   81 (92)
T d1aisa1           3 DMSKVKLRIENIVASVDLFAQLDLEKVLDLC-PNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVA   81 (92)
T ss_dssp             CCTTCEEEEEEEEEEEECCSCCCHHHHTTTS-TTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHH
T ss_pred             CcCcCcEEEEEEEEEEECCCCccHHHHHhhC-CCCEECcccCCeEEEEeCCCcEEEEEECCCEEEEEccCCHHHHHHHHH
Confidence            3456689999999999999999999999877 689999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 031013          154 NIYPVLTEF  162 (167)
Q Consensus       154 ~i~~~L~~~  162 (167)
                      +++++|+++
T Consensus        82 ~i~~~l~~l   90 (92)
T d1aisa1          82 KLAQKLKSI   90 (92)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHc
Confidence            999999875

>d1mp9a1 d.129.1.1 (A:5-96) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=100.00  E-value=1.7e-33  Score=201.11  Aligned_cols=84  Identities=39%  Similarity=0.653  Sum_probs=81.0

Q ss_pred             cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013           78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP  157 (167)
Q Consensus        78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~  157 (167)
                      ..++|+|||||++++++|||++||..+ ++++||||+||||+||+.+|+++++||+||||+||||||++++++|++++++
T Consensus         7 ~~~~i~NiVas~~l~~~idL~~la~~~-~~~~YePe~fpgli~R~~~p~~t~lIF~SGkivitGaks~~~~~~a~~~~~~   85 (92)
T d1mp9a1           7 AVVNIENIVATVTLDQTLDLYAMERSV-PNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIK   85 (92)
T ss_dssp             CEEEEEEEEEEEECCSCCCHHHHHHHS-TTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHHH
T ss_pred             CeEEEEEEEEEEECCCcccHHHHHhhC-CCCEECCccCceEEEEECCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHH
Confidence            368999999999999999999999988 6899999999999999999999999999999999999999999999999999


Q ss_pred             HHHhh
Q 031013          158 VLTEF  162 (167)
Q Consensus       158 ~L~~~  162 (167)
                      +|+++
T Consensus        86 ~L~~~   90 (92)
T d1mp9a1          86 TLKKY   90 (92)
T ss_dssp             HHHHT
T ss_pred             HHHHc
Confidence            99876

>d1qnaa1 d.129.1.1 (A:17-115) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=100.00  E-value=6.2e-33  Score=200.77  Aligned_cols=85  Identities=31%  Similarity=0.483  Sum_probs=81.2

Q ss_pred             cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013           78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP  157 (167)
Q Consensus        78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~  157 (167)
                      ..++|+|||||++++++|||++||..+ ++++||||+||||+||+.+|+++++||+||||+||||||++++++|++++++
T Consensus         5 ~~p~i~NiVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~R~~~P~~t~lIF~SGKivitGaks~~~~~~a~~~i~~   83 (99)
T d1qnaa1           5 IVPTLQNIVSTVNLDCKLDLKAIALQA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYAR   83 (99)
T ss_dssp             CCCEEEEEEEEEECCSCCCHHHHHHHC-SSEEECTTTCSEEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEEEcCCcccHHHHHhhC-CCCEECcccCCEEEEEeCCCcEEEEEEcCCEEEEeccCCHHHHHHHHHHHHH
Confidence            357999999999999999999999987 6999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhh
Q 031013          158 VLTEFR  163 (167)
Q Consensus       158 ~L~~~r  163 (167)
                      +|+++.
T Consensus        84 ~l~k~g   89 (99)
T d1qnaa1          84 IVQKLG   89 (99)
T ss_dssp             HHHHTT
T ss_pred             HHHHcC
Confidence            999863

>d1qnaa1 d.129.1.1 (A:17-115) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.90  E-value=3.3e-24  Score=154.51  Aligned_cols=73  Identities=85%  Similarity=1.227  Sum_probs=71.0

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      +++.|+|+|||||++++++|||++||..++|++|||+                        +||||+|+++++.|+++++
T Consensus         3 ~~~~p~i~NiVas~~l~~~idL~~la~~~~n~eYePe~fpgli~R~~~P~~t~lIF~SGKivitGaks~~~~~~a~~~i~   82 (99)
T d1qnaa1           3 SGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYA   82 (99)
T ss_dssp             TSCCCEEEEEEEEEECCSCCCHHHHHHHCSSEEECTTTCSEEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCcEEEEEEEEEEcCCcccHHHHHhhCCCCEECcccCCEEEEEeCCCcEEEEEEcCCEEEEeccCCHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999                        8999999999999999999


Q ss_pred             HHHHhcCCCCcccceEE
Q 031013           66 RIIQKLGFPAKFKDFKI   82 (167)
Q Consensus        66 ~~l~~lg~~~~~~~~~I   82 (167)
                      ++|+++|+++++.+|+|
T Consensus        83 ~~l~k~g~~v~~~~f~i   99 (99)
T d1qnaa1          83 RIVQKLGFPAKFKDFKI   99 (99)
T ss_dssp             HHHHHTTCCCCCEEEEE
T ss_pred             HHHHHcCCCCcccccCC
Confidence            99999999999999987

>d1mp9a1 d.129.1.1 (A:5-96) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=99.76  E-value=8e-19  Score=124.32  Aligned_cols=63  Identities=40%  Similarity=0.584  Sum_probs=60.2

Q ss_pred             CCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHH
Q 031013           11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYAR   66 (167)
Q Consensus        11 ~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~   66 (167)
                      ...++|+|||||++++++|||.+||..++|++|||+                        +||||+|+++++.|++++.+
T Consensus         6 ~~~~~i~NiVas~~l~~~idL~~la~~~~~~~YePe~fpgli~R~~~p~~t~lIF~SGkivitGaks~~~~~~a~~~~~~   85 (92)
T d1mp9a1           6 KAVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIK   85 (92)
T ss_dssp             CCEEEEEEEEEEEECCSCCCHHHHHHHSTTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEEEEECCCcccHHHHHhhCCCCEECCccCceEEEEECCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHH
Confidence            356899999999999999999999999999999999                        89999999999999999999


Q ss_pred             HHHhcCC
Q 031013           67 IIQKLGF   73 (167)
Q Consensus        67 ~l~~lg~   73 (167)
                      +|+++|.
T Consensus        86 ~L~~~G~   92 (92)
T d1mp9a1          86 TLKKYGM   92 (92)
T ss_dssp             HHHHTTC
T ss_pred             HHHHcCC
Confidence            9999995

>d1aisa1 d.129.1.1 (A:1-92) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.75  E-value=1.7e-18  Score=122.72  Aligned_cols=63  Identities=38%  Similarity=0.528  Sum_probs=60.8

Q ss_pred             CCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHH
Q 031013           11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYAR   66 (167)
Q Consensus        11 ~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~   66 (167)
                      .+.++|+||||++++++++||++|+..++|++|||+                        +||||+|+++++.|++++.+
T Consensus         6 ~~~~~I~NiVas~~l~~~idL~~la~~~~~~~YePe~fpgl~~R~~~p~~~~lIF~sGkivitGakS~~~~~~a~~~i~~   85 (92)
T d1aisa1           6 KVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQ   85 (92)
T ss_dssp             TCEEEEEEEEEEEECCSCCCHHHHTTTSTTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred             cCcEEEEEEEEEEECCCCccHHHHHhhCCCCEECcccCCeEEEEeCCCcEEEEEECCCEEEEEccCCHHHHHHHHHHHHH
Confidence            578999999999999999999999999999999999                        89999999999999999999


Q ss_pred             HHHhcCC
Q 031013           67 IIQKLGF   73 (167)
Q Consensus        67 ~l~~lg~   73 (167)
                      +|+++|.
T Consensus        86 ~l~~lGv   92 (92)
T d1aisa1          86 KLKSIGV   92 (92)
T ss_dssp             HHHHTTC
T ss_pred             HHHHcCC
Confidence            9999984

>d1aisa2 d.129.1.1 (A:93-181) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=99.71  E-value=9.2e-18  Score=118.20  Aligned_cols=61  Identities=36%  Similarity=0.535  Sum_probs=57.9

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      ....++|+|||||++++++|||++||..++|++|||+                        +||||+|+++++.|++++.
T Consensus         4 ~~p~i~I~NiVas~~l~~~idL~~la~~~~~~~Y~Pe~fpgli~R~~~p~~t~lIF~SGKivitGaks~~~~~~a~~~i~   83 (89)
T d1aisa2           4 RAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLL   83 (89)
T ss_dssp             SSCEEEEEEEEEEEECSSCCCHHHHHHHSTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCeEEEEEEEEEEECCCcccHHHHHhhccCcEECcccCceEEEEEcCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHH
Confidence            3456799999999999999999999999999999999                        9999999999999999999


Q ss_pred             HHHHh
Q 031013           66 RIIQK   70 (167)
Q Consensus        66 ~~l~~   70 (167)
                      ++|++
T Consensus        84 ~~L~k   88 (89)
T d1aisa2          84 RELDK   88 (89)
T ss_dssp             HHHTT
T ss_pred             HHHhc
Confidence            99986

>d1mp9a2 d.129.1.1 (A:97-197) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=99.67  E-value=5.5e-17  Score=116.61  Aligned_cols=64  Identities=31%  Similarity=0.404  Sum_probs=61.0

Q ss_pred             cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013           10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA   65 (167)
Q Consensus        10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~   65 (167)
                      +....+|+||||+++++++|||++||..++|++|||+                        +||||+|+++++.|++++.
T Consensus         4 ~~p~~~v~NiVas~~l~~~idL~~la~~~~~~~YePe~fpgli~R~~~pk~t~lIF~SGKivitGaks~~~~~~a~~~i~   83 (101)
T d1mp9a2           4 GKPKIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIF   83 (101)
T ss_dssp             SCCEEEEEEEEEEEECSSEECHHHHHHHSSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEEEEEEECCCcccHHHHHhhCCCCEECcccCCeEEEEecCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999                        8999999999999999999


Q ss_pred             HHHHhcCC
Q 031013           66 RIIQKLGF   73 (167)
Q Consensus        66 ~~l~~lg~   73 (167)
                      ++|+++|.
T Consensus        84 ~~L~~~~~   91 (101)
T d1mp9a2          84 DKLVELDC   91 (101)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHhCC
Confidence            99999985

>d1qnaa2 d.129.1.1 (A:116-198) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a+b)
fold: TBP-like
superfamily: TATA-box binding protein-like
family: TATA-box binding protein (TBP), C-terminal domain
domain: TATA-box binding protein (TBP), C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.54  E-value=4.9e-15  Score=102.67  Aligned_cols=55  Identities=24%  Similarity=0.405  Sum_probs=52.2

Q ss_pred             EEEEEEEEeCCccchHhHHhhCC-CceecCC------------------------ceeccCCHHHHHHHHHHHHHHHHhc
Q 031013           17 KNIVSTVNLDCKLDLKKIALQAR-NAEYNPK------------------------VCTGAKSEQQSKLAARKYARIIQKL   71 (167)
Q Consensus        17 ~NVV~s~~l~~~ldL~~ia~~~~-n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l~~l   71 (167)
                      +|||||++++++|||++||...+ |++|||+                        +||||+|+++++.|++++.++|+++
T Consensus         1 qNiVas~~l~~~I~L~~la~~~~~~~~YePe~fpgl~~R~~~pk~~~lIF~SGkivitGaks~~~~~~a~~~i~~~L~~~   80 (83)
T d1qnaa2           1 QNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEF   80 (83)
T ss_dssp             EEEEEEEECSSCBCHHHHHHHTTTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCCCccHHHHHHhhhhhcccChhhCCeEEEEECCCCeEEEEEcCCEEEEECCCCHHHHHHHHHHHHHHHHHh
Confidence            79999999999999999999875 7999999                        9999999999999999999999875