Citrus Sinensis ID: 047239

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180
Protein Sequence
MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ
Secondary Structure (PSIPRED)
cccEEEEEEEEEEEcccccHHHHHHHccccEEccccccEEEEEEccccEEEEEEEccEEEEEEcccHHHHHHHHHHHHHHHHHccccccccccEEEEEEEEEEccccccHHHHHHcccccccccccccccEEEEEccccEEEEEEcccEEEEEEEccHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEEEEccccccHHHHHHHcccEEEEcccEEEEEEEEccccEEEEEccccEEEEEEEccHHHHHHHHHHHHHHHHHcccccccEEEEEEEEEEEEEccccEcHHHHHHHccccEEccccccccEEEEEccccEEEEEccccEEEEEEEccHHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MAPVIQNIVATINLECKLDLKKIALHARnaeynpsrfsAVTMrikepkttalifssgkivctgakSESQAKLAARKYARIVQkigfpvqfkdfkiqnivgscdvefpiklerlngfhamfstyepelfpgliyrmkkpnvTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ
Flexible Loop (DISEMBL)
MAPVIQNIVATINLECKLDLKKIALHarnaeynpsrfsavTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ
Low Complexity Region (SEG)
MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ
Disordered region (IsUnstruct)
***VIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTY**
Disordered Region (DISOPRED)
MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVT***
Disordered Region (DISEMBL)
MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAK********ARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ
Disordered Region (DISPRO)
MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYV****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ
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	180	2.2.26 [Sep-21-2011]
P50159	200	TATA-box-binding protein	N/A	no	1.0	0.9	0.722	4e-76
P50158	200	TATA-box-binding protein	N/A	no	0.955	0.86	0.75	6e-76
P26356	233	TATA-box-binding protein	N/A	no	0.972	0.751	0.731	7e-76
P26357	200	TATA-box-binding protein	N/A	no	0.972	0.875	0.737	8e-76
P48511	200	TATA-box-binding protein	N/A	no	0.972	0.875	0.737	8e-76
Q8W0W4	203	TATA-binding protein 2 OS	yes	no	0.988	0.876	0.724	1e-75
Q02879	201	TATA-box-binding protein	N/A	no	0.988	0.885	0.719	2e-75
Q42808	200	TATA-box-binding protein	yes	no	0.972	0.875	0.725	3e-75
Q5UE94	320	TATA box-binding protein-	N/A	no	0.955	0.537	0.744	5e-75
P28148	200	TATA-box-binding protein	yes	no	1.0	0.9	0.727	5e-75

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

 Score =  283 bits (724), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 155/180 (86%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL+ +    Q
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLSEFRKIQQ 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|P50158|TBP1_MAIZE TATA-box-binding protein 1 OS=Zea mays GN=TBP1 PE=2 SV=1

 Score =  283 bits (723), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 129/172 (75%), Positives = 152/172 (88%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVL 192

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

 Score =  282 bits (722), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 128/175 (73%), Positives = 154/175 (88%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + PV+QNIV+T+NL+C+LDLK+IAL ARNAEYNP RF+AV MRI++PKTTALIF+SGK+V
Sbjct: 54  IVPVLQNIVSTVNLDCRLDLKQIALQARNAEYNPKRFAAVIMRIRDPKTTALIFASGKMV 113

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE  +KLAARKYARIVQK+GFP  FKDFKIQNIV SCDV+FPI+LE L   H  F
Sbjct: 114 CTGAKSEEHSKLAARKYARIVQKLGFPATFKDFKIQNIVASCDVKFPIRLEGLAYSHGAF 173

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRMK+P + +L+F+SGK+V+TGAK R++IYAAF NIYPVL  Y
Sbjct: 174 SSYEPELFPGLIYRMKQPKIVLLVFVSGKIVLTGAKVRDEIYAAFENIYPVLTEY 228

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

 Score =  282 bits (722), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 129/175 (73%), Positives = 153/175 (87%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRMK+P + +LIF+SGK+VITGAK R++ Y AF NIYPVL  +
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 195

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

 Score =  282 bits (721), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 129/175 (73%), Positives = 153/175 (87%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL  +
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEF 195

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

 Score =  281 bits (720), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 129/178 (72%), Positives = 153/178 (85%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+VCT
Sbjct: 26  PTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCT 85

Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  FS+
Sbjct: 86  GAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSS 145

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK R++ Y AF NIYPVL  +    Q
Sbjct: 146 YEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEFRKVQQ 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|Q02879|TBP2_WHEAT TATA-box-binding protein 2 OS=Triticum aestivum GN=TBP2 PE=2 SV=1

 Score =  281 bits (718), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 128/178 (71%), Positives = 153/178 (85%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+VCT
Sbjct: 24  PTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCT 83

Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIV SCDV+FPI+LE L   H  FS+
Sbjct: 84  GAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVASCDVKFPIRLEGLAYSHGAFSS 143

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           YEPELFPGLIYRM++P + +LIF+SGK+V+TGAK RE+ Y+AF NIYPVL  +    Q
Sbjct: 144 YEPELFPGLIYRMRQPKIVLLIFVSGKIVLTGAKVREETYSAFENIYPVLTEFRKVQQ 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|Q42808|TBP_SOYBN TATA-box-binding protein OS=Glycine max GN=TBP1 PE=2 SV=1

 Score =  280 bits (717), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 127/175 (72%), Positives = 153/175 (87%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI++PKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKTIALQARNAEYNPKRFAAVIMRIRDPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK R++ Y AF NIYPVL  +
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDETYTAFENIYPVLTEF 195

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|Q5UE94|TBPL2_XENLA TATA box-binding protein-like protein 2 OS=Xenopus laevis GN=tbpl2 PE=2 SV=1

 Score =  280 bits (715), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 128/172 (74%), Positives = 150/172 (87%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL CKLDLKKIALHARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct: 142 IVPQLQNIVSTVNLACKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 201

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV FPI+LE L   H  F
Sbjct: 202 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVRFPIRLEGLVLTHQQF 261

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct: 262 SSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTGAKERSEIYEAFENIYPIL 313

TATA box-binding transcription factor. Members of the TBP family are differentially required to regulate transcription and development during early embryogenesis. Required for gastrulation. Regulates a large subset of genes that are ventrally expressed. Binds to a subset of promoters.

Xenopus laevis (taxid: 8355)

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

 Score =  280 bits (715), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 131/180 (72%), Positives = 153/180 (85%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE  +KLAARKYARIVQK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H+ F
Sbjct: 81  CTGAKSEHLSKLAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHSAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK P + +LIF+SGK+VITGAK RE+ Y AF NIYPVL  +    Q
Sbjct: 141 SSYEPELFPGLIYRMKLPKIVLLIFVSGKIVITGAKMREETYTAFENIYPVLREFRKVQQ 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)

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	180
302758308	199	hypothetical protein SELMODRAFT_270329 [	0.988	0.894	0.735	1e-75
168003287	214	TATA-box binding protein, component of T	1.0	0.841	0.716	8e-75
255568956	201	TATA-box binding protein, putative [Rici	1.0	0.895	0.722	1e-74
357155673	202	PREDICTED: TATA-box-binding protein 2-li	1.0	0.891	0.716	2e-74
357119735	200	PREDICTED: TATA-box-binding protein 2-li	0.988	0.89	0.730	2e-74
162459971	200	TATA-box-binding protein 2 [Zea mays] gi	1.0	0.9	0.722	2e-74
242038657	200	hypothetical protein SORBIDRAFT_01g01288	1.0	0.9	0.722	2e-74
413933539	205	TATA-binding protein2, partial [Zea mays	1.0	0.878	0.722	3e-74
974216	215	TATA-box binding protein [Zea mays]	0.955	0.8	0.75	3e-74
449452638	200	PREDICTED: TATA-box-binding protein-like	0.972	0.875	0.737	3e-74

>gi|302758308|ref|XP_002962577.1| hypothetical protein SELMODRAFT_270329 [Selaginella moellendorffii] gi|302824582|ref|XP_002993933.1| hypothetical protein SELMODRAFT_163230 [Selaginella moellendorffii] gi|300138205|gb|EFJ04980.1| hypothetical protein SELMODRAFT_163230 [Selaginella moellendorffii] gi|300169438|gb|EFJ36040.1| hypothetical protein SELMODRAFT_270329 [Selaginella moellendorffii]

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 131/178 (73%), Positives = 155/178 (87%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QNIV+T+N++CKLDLK IALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+VCT
Sbjct: 22  PTLQNIVSTVNMDCKLDLKTIALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCT 81

Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE Q+KLAARKYARI+QK+GFP QFKDFKIQNIVGSCDV+FPI+LE L   H  FS+
Sbjct: 82  GAKSEQQSKLAARKYARIIQKLGFPAQFKDFKIQNIVGSCDVKFPIRLEGLAYAHGHFSS 141

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK R++IY AF NIYPVL  +    Q
Sbjct: 142 YEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDEIYEAFENIYPVLTEFRKMQQ 199

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168003287|ref|XP_001754344.1| TATA-box binding protein, component of TFIID and TFIIIB [Physcomitrella patens subsp. patens] gi|162694446|gb|EDQ80794.1| TATA-box binding protein, component of TFIID and TFIIIB [Physcomitrella patens subsp. patens]

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 129/180 (71%), Positives = 156/180 (86%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+N++C+L+LK IALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNMDCRLELKTIALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP QFKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAQFKDFKIQNIVGSCDVKFPIRLEGLAYAHGHF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK R++IY AF NIYPVL  +    Q
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVRDEIYEAFENIYPVLTEFRKIQQ 200

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  283 bits (725), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 155/180 (86%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK+IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 22  IVPTLQNIVSTVNLDCKLDLKQIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 81

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 82  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 141

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK+P + +LIF+SGK+VITGAK R++ Y AF NIYPVL  +    Q
Sbjct: 142 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQQ 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 129/180 (71%), Positives = 155/180 (86%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P++QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 23  IVPMLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 82

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 83  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 142

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRM++P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL  +    Q
Sbjct: 143 SSYEPELFPGLIYRMRQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKVQQ 202

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

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 =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 130/178 (73%), Positives = 153/178 (85%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+VCT
Sbjct: 23  PTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCT 82

Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  FS+
Sbjct: 83  GAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSS 142

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL  +    Q
Sbjct: 143 YEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKVQQ 200

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|162459971|ref|NP_001105319.1| TATA-box-binding protein 2 [Zea mays] gi|1729908|sp|P50159.1|TBP2_MAIZE RecName: Full=TATA-box-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|293906|gb|AAA65942.1| TATA-binding protein [Zea mays] gi|195604414|gb|ACG24037.1| TATA-binding protein 2 [Zea mays] gi|238014342|gb|ACR38206.1| unknown [Zea mays] gi|413933540|gb|AFW68091.1| TATA-binding protein2 [Zea mays]

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 155/180 (86%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL+ +    Q
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLSEFRKIQQ 200

Source: Zea mays

Species: Zea mays

Genus: Zea

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 =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 154/180 (85%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL  +    Q
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEFRKVQQ 200

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413933539|gb|AFW68090.1| TATA-binding protein2, partial [Zea mays]

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 155/180 (86%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL+ +    Q
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLSEFRKIQQ 200

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|974216|emb|CAA62224.1| TATA-box binding protein [Zea mays]

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 129/172 (75%), Positives = 152/172 (88%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVL 192

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452638|ref|XP_004144066.1| PREDICTED: TATA-box-binding protein-like [Cucumis sativus] gi|449493574|ref|XP_004159356.1| PREDICTED: TATA-box-binding protein-like [Cucumis sativus]

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 129/175 (73%), Positives = 153/175 (87%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q+KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 81  CTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAF 140

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRMK+P + +LIF+SGK+V+TGAK RE+ Y AF NIYPVL  +
Sbjct: 141 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVLTGAKVREETYTAFENIYPVLTEF 195

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	180
TAIR|locus:2193904	200	TBP2 "TATA binding protein 2"	0.972	0.875	0.742	7.2e-68
TAIR|locus:2092905	200	TBP1 "TATA binding protein 1"	0.972	0.875	0.737	1.2e-67
UNIPROTKB|Q28DH2	322	tbpl2 "TATA box-binding protei	0.955	0.534	0.744	2.4e-67
UNIPROTKB|Q5UE94	320	tbpl2 "TATA box-binding protei	0.955	0.537	0.744	2.4e-67
UNIPROTKB|Q6SJ96	375	TBPL2 "TATA box-binding protei	0.955	0.458	0.738	5.1e-67
UNIPROTKB|F1NEQ8	321	TBPL2 "Uncharacterized protein	0.955	0.535	0.738	8.2e-67
UNIPROTKB|F1PVR2	376	TBPL2 "Uncharacterized protein	0.955	0.457	0.732	5.8e-66
UNIPROTKB|O13270	302	TBP "TATA-box-binding protein"	0.955	0.569	0.732	9.4e-66
UNIPROTKB|Q6JLB1	302	TBP "TATA-binding protein" [Ga	0.955	0.569	0.732	9.4e-66
UNIPROTKB|Q2HJ52	319	TBP "TATA-box-binding protein"	0.955	0.539	0.732	9.4e-66

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

 Score = 689 (247.6 bits), Expect = 7.2e-68, P = 7.2e-68
 Identities = 130/175 (74%), Positives = 152/175 (86%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct:    21 IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE  +KLAARKYARIVQK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H+ F
Sbjct:    81 CTGAKSEHLSKLAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHSAF 140

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
             S+YEPELFPGLIYRMK P + +LIF+SGK+VITGAK RE+ Y AF NIYPVL  +
Sbjct:   141 SSYEPELFPGLIYRMKLPKIVLLIFVSGKIVITGAKMREETYTAFENIYPVLREF 195

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 = 687 (246.9 bits), Expect = 1.2e-67, P = 1.2e-67
 Identities = 129/175 (73%), Positives = 153/175 (87%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct:    21 IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE  +K+AARKYARIVQK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   HA F
Sbjct:    81 CTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAF 140

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
             S+YEPELFPGLIYRMK P + +LIF+SGK+VITGAK R++ Y AF NIYPVL+ +
Sbjct:   141 SSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEF 195

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

UNIPROTKB|Q28DH2 tbpl2 "TATA box-binding protein-like protein 2" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 128/172 (74%), Positives = 150/172 (87%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLKKIALHARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   144 IVPQLQNIVSTVNLACKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 203

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV FPI+LE L   H  F
Sbjct:   204 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVRFPIRLEGLVLTHQQF 263

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   264 SSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTGAKERSEIYEAFENIYPIL 315

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0007369 "gastrulation" evidence=ISS

GO:0009790 "embryo development" evidence=ISS

UNIPROTKB|Q5UE94 tbpl2 "TATA box-binding protein-like protein 2" [Xenopus laevis (taxid:8355)]

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 128/172 (74%), Positives = 150/172 (87%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLKKIALHARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   142 IVPQLQNIVSTVNLACKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 201

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV FPI+LE L   H  F
Sbjct:   202 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVRFPIRLEGLVLTHQQF 261

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   262 SSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTGAKERSEIYEAFENIYPIL 313

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007369 "gastrulation" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

UNIPROTKB|Q6SJ96 TBPL2 "TATA box-binding protein-like protein 2" [Homo sapiens (taxid:9606)]

 Score = 681 (244.8 bits), Expect = 5.1e-67, P = 5.1e-67
 Identities = 127/172 (73%), Positives = 150/172 (87%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLKKIALHA+NAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   198 IVPQLQNIVSTVNLACKLDLKKIALHAKNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 257

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV FPI+LE L   H  F
Sbjct:   258 CTGAKSEEQSRLAARKYARVVQKLGFPARFLDFKIQNMVGSCDVRFPIRLEGLVLTHQQF 317

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   318 SSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTGAKERSEIYEAFENIYPIL 369

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1NEQ8 TBPL2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 679 (244.1 bits), Expect = 8.2e-67, P = 8.2e-67
 Identities = 127/172 (73%), Positives = 149/172 (86%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLK IALHARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   143 IVPQLQNIVSTVNLACKLDLKNIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 202

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV FPI+LE L   H  F
Sbjct:   203 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVRFPIRLEGLVLTHQQF 262

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   263 SSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTGAKERSEIYEAFENIYPIL 314

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

UNIPROTKB|F1PVR2 TBPL2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 126/172 (73%), Positives = 148/172 (86%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLKKIALHA+NAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   199 IVPQLQNIVSTVNLACKLDLKKIALHAKNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 258

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV F I LE L   H  F
Sbjct:   259 CTGAKSEEQSRLAARKYARVVQKLGFPARFLDFKIQNMVGSCDVRFAISLEGLVLTHQQF 318

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   319 SSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTGAKERSEIYEAFENIYPIL 370

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

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 126/172 (73%), Positives = 149/172 (86%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   124 IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 183

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct:   184 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 243

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   244 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPIL 295

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 = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 126/172 (73%), Positives = 149/172 (86%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   124 IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 183

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct:   184 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 243

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   244 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPIL 295

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 = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 126/172 (73%), Positives = 149/172 (86%)

Query:     1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
             + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct:   141 IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 200

Query:    61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
             CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct:   201 CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 260

Query:   121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
             S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct:   261 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPIL 312

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P13393	TBP_YEAST	No assigned EC number	0.7085	0.9722	0.7291	yes	no
P93348	TBP_TOBAC	No assigned EC number	0.72	0.9722	0.875	N/A	no
P50159	TBP2_MAIZE	No assigned EC number	0.7222	1.0	0.9	N/A	no
P50158	TBP1_MAIZE	No assigned EC number	0.75	0.9555	0.86	N/A	no
P91809	TBP_STRPU	No assigned EC number	0.7142	0.9722	0.6603	yes	no
O43133	TBP_CANAL	No assigned EC number	0.7109	0.9611	0.7268	N/A	no
P26356	TBP1_WHEAT	No assigned EC number	0.7314	0.9722	0.7510	N/A	no
P26357	TBP_SOLTU	No assigned EC number	0.7371	0.9722	0.875	N/A	no
P26354	TBP_ACACA	No assigned EC number	0.7142	0.9722	0.6782	N/A	no
P26355	TBP_DICDI	No assigned EC number	0.6936	0.9611	0.8439	yes	no
P46272	TBP_ACECL	No assigned EC number	0.6705	0.9611	0.9057	N/A	no
O17488	TBP_ARTSF	No assigned EC number	0.7352	0.9444	0.6181	N/A	no
C4M7H7	TBP2_ENTHI	No assigned EC number	0.5588	0.9444	0.8018	N/A	no
Q42808	TBP_SOYBN	No assigned EC number	0.7257	0.9722	0.875	yes	no
A6H907	TBPL2_PANTR	No assigned EC number	0.7383	0.9555	0.4574	yes	no
P28148	TBP2_ARATH	No assigned EC number	0.7277	1.0	0.9	yes	no
P32085	TBP_CAEEL	No assigned EC number	0.7176	0.9444	0.5	yes	no
Q12731	TBP_EMENI	No assigned EC number	0.7167	0.9611	0.6455	yes	no
P29037	TBP_MOUSE	No assigned EC number	0.72	0.9722	0.5537	yes	no
P28147	TBP1_ARATH	No assigned EC number	0.7222	1.0	0.9	no	no
Q8W0W4	TBP2_ORYSJ	No assigned EC number	0.7247	0.9888	0.8768	yes	no
A1RSQ1	TBP_PYRIL	No assigned EC number	0.4642	0.9	0.8140	yes	no
Q6SJ96	TBPL2_HUMAN	No assigned EC number	0.7383	0.9555	0.4586	yes	no
P17871	TBP_SCHPO	No assigned EC number	0.7028	0.9722	0.7575	yes	no
Q2HJ52	TBP_BOVIN	No assigned EC number	0.72	0.9722	0.5485	yes	no
P48511	TBP_MESCR	No assigned EC number	0.7371	0.9722	0.875	N/A	no
Q28DH2	TBPL2_XENTR	No assigned EC number	0.7441	0.9555	0.5341	yes	no
P20227	TBP_DROME	No assigned EC number	0.7167	0.9611	0.4900	yes	no
Q02879	TBP2_WHEAT	No assigned EC number	0.7191	0.9888	0.8855	N/A	no
Q7SXL3	TBP_DANRE	No assigned EC number	0.72	0.9722	0.5794	yes	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:
	GTF1502.2	TATA-box binding protein, component of TFIID and TFIIIB (214 aa)
		(Physcomitrella patens)
Predicted Functional Partners:
	JGI138531	hypothetical protein (312 aa)	•		•		•	•	•		0.961
	JGI120732	hypothetical protein (312 aa)			•		•	•	•		0.900
	JGI110527	hypothetical protein (149 aa)					•	•	•		0.666
	TAFV1501	TFIID and SAGA complex subunit (673 aa)					•	•	•		0.642
	JGI57083	hypothetical protein (525 aa)					•	•	•		0.634
	JGI187813	hypothetical protein (73 aa)						•	•		0.605
	JGI53971	hypothetical protein (125 aa)					•	•	•		0.591
	JGI178304	hypothetical protein (106 aa)					•	•	•		0.581
	JGI142855	hypothetical protein (119 aa)	•					•	•		0.571
	CHR1532	SNF2 superfamily chromatin remodeling protein (2041 aa)					•		•		0.567

---

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	180
cd04516	174	cd04516, TBP_eukaryotes, eukaryotic TATA box bindi	1e-111
PLN00062	179	PLN00062, PLN00062, TATA-box-binding protein; Prov	1e-110
cd00652	174	cd00652, TBP_TLF, TATA box binding protein (TBP):	3e-99
COG2101	185	COG2101, SPT15, TATA-box binding protein (TBP), co	8e-75
cd04517	174	cd04517, TLF, TBP-like factors (TLF; also called T	9e-63
PRK00394	179	PRK00394, PRK00394, transcription factor; Reviewed	7e-58
cd04518	174	cd04518, TBP_archaea, archaeal TATA box binding pr	1e-49
pfam00352	86	pfam00352, TBP, Transcription factor TFIID (or TAT	3e-41
pfam00352	86	pfam00352, TBP, Transcription factor TFIID (or TAT	2e-34
PRK00394	179	PRK00394, PRK00394, transcription factor; Reviewed	2e-24
cd04518	174	cd04518, TBP_archaea, archaeal TATA box binding pr	3e-23
COG2101	185	COG2101, SPT15, TATA-box binding protein (TBP), co	4e-20
cd00652	174	cd00652, TBP_TLF, TATA box binding protein (TBP):	2e-19
PRK00394	179	PRK00394, PRK00394, transcription factor; Reviewed	2e-19
COG2101	185	COG2101, SPT15, TATA-box binding protein (TBP), co	8e-18
cd04518	174	cd04518, TBP_archaea, archaeal TATA box binding pr	7e-16
cd00652	174	cd00652, TBP_TLF, TATA box binding protein (TBP):	3e-15

>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 =  313 bits (805), Expect = e-111
 Identities = 131/171 (76%), Positives = 150/171 (87%)

Query: 2   APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVC 61
            P IQNIVAT+NL CKLDLKKIAL ARNAEYNP RF+AV MRI+EPKTTALIFSSGK+VC
Sbjct: 1   VPKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVC 60

Query: 62  TGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFS 121
           TGAKSE  +KLAARKYARI+QK+GFP +F DFKIQNIVGSCDV+FPI+LE L   H  FS
Sbjct: 61  TGAKSEDDSKLAARKYARIIQKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFS 120

Query: 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           +YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK+RE+IY AF NIYP+L
Sbjct: 121 SYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIYQAFENIYPIL 171

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|177693 PLN00062, PLN00062, TATA-box-binding protein; Provisional

 Score =  310 bits (797), Expect = e-110
 Identities = 131/171 (76%), Positives = 152/171 (88%)

Query: 2   APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVC 61
            P +QNIV+T+NL+CKLDLKKIAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+VC
Sbjct: 1   VPTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVC 60

Query: 62  TGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFS 121
           TGAKSE  +KLAARKYARI+QK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   H  FS
Sbjct: 61  TGAKSEHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFS 120

Query: 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           +YEPELFPGLIYRMK+P + +LIF+SGK+VITGAK RE+IY AF NIYPVL
Sbjct: 121 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYPVL 171

Length = 179

>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 =  283 bits (726), Expect = 3e-99
 Identities = 121/172 (70%), Positives = 142/172 (82%), Gaps = 1/172 (0%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P IQNIVAT+NL C+LDL+KIAL ARNAEYNP RF  V MR++EPKTTALIFSSGK+V T
Sbjct: 2   PKIQNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVIT 61

Query: 63  GAKSESQAKLAARKYARIVQKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFS 121
           GAKSE  AKLAARKYARI+QK+GFPV +F +FK+QNIV SCD+ FPI+LE L   H   +
Sbjct: 62  GAKSEEDAKLAARKYARILQKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENA 121

Query: 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLN 173
           +YEPELFPGLIYRM +P V +LIF+SGK+VITGAK+RE IY A   IYP+L 
Sbjct: 122 SYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILK 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. 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 =  221 bits (566), Expect = 8e-75
 Identities = 76/174 (43%), Positives = 109/174 (62%), Gaps = 2/174 (1%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
               I+NIVA+++L  +LDL+++AL    AEYNP +F  +  R++EPKT ALIF SGK+V
Sbjct: 6   PTITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVV 65

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLERLNGFHAM 119
           CTGAKS      A +K A+ ++  G  + F+ + K+QNIV S D+   + L  +     +
Sbjct: 66  CTGAKSVEDVHRAVKKLAKKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGL 125

Query: 120 FST-YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
            +  YEPE FPGL+YR+ +P V +L+F SGK+VITGAK+ E    A   I   L
Sbjct: 126 ENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRL 179

Length = 185

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

 Score =  191 bits (486), Expect = 9e-63
 Identities = 79/171 (46%), Positives = 120/171 (70%), Gaps = 2/171 (1%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
            +I N+V   +L C +DL+K+AL  RN EYNP R+  VTMR++EP+ TA ++SSGKI  T
Sbjct: 3   ILIVNVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITIT 61

Query: 63  GAKSESQAKLAARKYARIVQKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFS 121
           GA SE +AK AAR+ AR++QK+GF V +F +F++ N++ +C + FPI+L+ L   +   +
Sbjct: 62  GATSEEEAKQAARRAARLLQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSA 121

Query: 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           +YEPEL PG++YR+  P  T+ IF +G V +TGA++ E +  A   IYP++
Sbjct: 122 SYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPIV 172

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|234746 PRK00394, PRK00394, transcription factor; Reviewed

 Score =  178 bits (455), Expect = 7e-58
 Identities = 73/167 (43%), Positives = 103/167 (61%), Gaps = 2/167 (1%)

Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I+NIVA+ +L  +LDL+K+A    NAEYNP +F  +  R+++PK  ALIF SGK+VCTGA
Sbjct: 3   IENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGA 62

Query: 65  KSESQAKLAARKYARIVQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLERLN-GFHAMFST 122
           KS      A +   + ++++G  V  + + K+QNIV S D+   + L  +  G       
Sbjct: 63  KSVEDLHEAVKIIIKKLKELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIE 122

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIY 169
           YEPE FPGL+YR+  P V +L+F SGK+VITGAK+ E    A   I 
Sbjct: 123 YEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKIL 169

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 =  157 bits (400), Expect = 1e-49
 Identities = 73/165 (44%), Positives = 104/165 (63%), Gaps = 10/165 (6%)

Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I+NIVA+++L  +LDL+K+A    NAEYNP +F  +  R+++PK  ALIF SGK+VCTGA
Sbjct: 4   IENIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGA 63

Query: 65  KSESQAKLAARKYARIVQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLER----LNGFHAM 119
           KS      A ++  + ++  G  V  K + K+QNIV S D+   + L+     L      
Sbjct: 64  KSVEDLHRAVKEIIKKLKDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLPN---- 119

Query: 120 FSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAA 164
            + YEPE FPGL+YR+ +P V +L+F SGK+VITGAK+ E    A
Sbjct: 120 -AEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRA 163

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

 Score =  133 bits (337), Expect = 3e-41
 Identities = 49/83 (59%), Positives = 61/83 (73%)

Query: 3  PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
            IQNIVA+ +L   +DL+KIAL  RNAEY P +F  +  R++EPK TALIFSSGK+V T
Sbjct: 4  IKIQNIVASADLGFPIDLEKIALKLRNAEYEPEQFPGLVYRLREPKATALIFSSGKVVIT 63

Query: 63 GAKSESQAKLAARKYARIVQKIG 85
          GAKSE  AK A RK A I++K+G
Sbjct: 64 GAKSEEDAKKAVRKIAPILKKLG 86

Length = 86

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

 Score =  116 bits (293), Expect = 2e-34
 Identities = 45/84 (53%), Positives = 55/84 (65%), Gaps = 1/84 (1%)

Query: 90  FKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGK 149
           F D KIQNIV S D+ FPI LE++       + YEPE FPGL+YR+++P  T LIF SGK
Sbjct: 1   FPDIKIQNIVASADLGFPIDLEKIA-LKLRNAEYEPEQFPGLVYRLREPKATALIFSSGK 59

Query: 150 VVITGAKAREQIYAAFNNIYPVLN 173
           VVITGAK+ E    A   I P+L 
Sbjct: 60  VVITGAKSEEDAKKAVRKIAPILK 83

Length = 86

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

 Score = 93.8 bits (234), Expect = 2e-24
 Identities = 35/83 (42%), Positives = 51/83 (61%), Gaps = 2/83 (2%)

Query: 5   IQNIVATINLECKLDLKKIA--LHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           +QNIVA+ +L  +L+L  IA  L   N EY P +F  +  R+ +PK   L+F SGK+V T
Sbjct: 94  VQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVIT 153

Query: 63  GAKSESQAKLAARKYARIVQKIG 85
           GAKSE  A+ A  K    ++++G
Sbjct: 154 GAKSEEDAEKAVEKILEKLEELG 176

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 = 90.4 bits (225), Expect = 3e-23
 Identities = 36/82 (43%), Positives = 52/82 (63%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
             +QNIVA+ +L  +++L  IA+   NAEY P +F  +  R+ EPK   L+FSSGK+V T
Sbjct: 93  IKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVIT 152

Query: 63  GAKSESQAKLAARKYARIVQKI 84
           GAKSE  AK A  K    ++++
Sbjct: 153 GAKSEEDAKRAVEKLLSRLKEL 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|225012 COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]

 Score = 82.4 bits (204), Expect = 4e-20
 Identities = 35/83 (42%), Positives = 51/83 (61%), Gaps = 2/83 (2%)

Query: 5   IQNIVATINLECKLDLKKIA--LHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           +QNIVA+ +L  +L+L  IA  L   N EY P +F  +  R+ EP+   L+F SGK+V T
Sbjct: 101 VQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVIT 160

Query: 63  GAKSESQAKLAARKYARIVQKIG 85
           GAKSE  A+ A  K    ++++G
Sbjct: 161 GAKSEEDAEQAVEKIQSRLEELG 183

Length = 185

>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 = 80.3 bits (199), Expect = 2e-19
 Identities = 35/80 (43%), Positives = 47/80 (58%), Gaps = 1/80 (1%)

Query: 5   IQNIVATINLECKLDLKKIAL-HARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTG 63
           +QNIVA+ +L   + L+++AL H  NA Y P  F  +  R+ EPK   LIF SGKIV TG
Sbjct: 95  VQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITG 154

Query: 64  AKSESQAKLAARKYARIVQK 83
           AKS      A  K   I+++
Sbjct: 155 AKSREDIYEAVEKIYPILKE 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|234746 PRK00394, PRK00394, transcription factor; Reviewed

 Score = 80.3 bits (199), Expect = 2e-19
 Identities = 35/78 (44%), Positives = 48/78 (61%), Gaps = 7/78 (8%)

Query: 94  KIQNIVGSCDVEFPIKLERLNGFHAM---FSTYEPELFPGLIYRMKKPNVTMLIFLSGKV 150
           KI+NIV S D+   + LE++    A     + Y PE FPGL+YR++ P +  LIF SGKV
Sbjct: 2   KIENIVASTDLGQELDLEKV----AEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKV 57

Query: 151 VITGAKAREQIYAAFNNI 168
           V TGAK+ E ++ A   I
Sbjct: 58  VCTGAKSVEDLHEAVKII 75

Length = 179

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

 Score = 76.3 bits (188), Expect = 8e-18
 Identities = 33/80 (41%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 94  KIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVIT 153
            I+NIV S D+   + LE +       + Y PE FPGL+YR+++P    LIF SGKVV T
Sbjct: 9   TIENIVASVDLGQELDLEEVA-LDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCT 67

Query: 154 GAKAREQIYAAFNNIYPVLN 173
           GAK+ E ++ A   +   L 
Sbjct: 68  GAKSVEDVHRAVKKLAKKLK 87

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 = 71.1 bits (175), Expect = 7e-16
 Identities = 32/73 (43%), Positives = 47/73 (64%), Gaps = 5/73 (6%)

Query: 94  KIQNIVGSCDVEFPIKLERLNGFHAMF--STYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
           KI+NIV S D+   + LE++    A    + Y P+ FPGL+YR++ P +  LIF SGK+V
Sbjct: 3   KIENIVASVDLGQELDLEKVA---AELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMV 59

Query: 152 ITGAKAREQIYAA 164
            TGAK+ E ++ A
Sbjct: 60  CTGAKSVEDLHRA 72

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 = 69.1 bits (170), Expect = 3e-15
 Identities = 30/69 (43%), Positives = 44/69 (63%), Gaps = 1/69 (1%)

Query: 92  DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
             KIQNIV + ++   + L ++    A  + Y P+ FPG+I R+++P  T LIF SGK+V
Sbjct: 1   SPKIQNIVATVNLGCELDLRKI-ALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMV 59

Query: 152 ITGAKAREQ 160
           ITGAK+ E 
Sbjct: 60  ITGAKSEED 68

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	180
PLN00062	179	TATA-box-binding protein; Provisional	100.0
cd04516	174	TBP_eukaryotes eukaryotic TATA box binding protein	100.0
KOG3302	200	consensus TATA-box binding protein (TBP), componen	100.0
COG2101	185	SPT15 TATA-box binding protein (TBP), component of	100.0
cd00652	174	TBP_TLF TATA box binding protein (TBP): Present in	100.0
PRK00394	179	transcription factor; Reviewed	100.0
cd04518	174	TBP_archaea archaeal TATA box binding protein (TBP	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	99.97
PF00352	86	TBP: Transcription factor TFIID (or TATA-binding p	99.97
COG2101	185	SPT15 TATA-box binding protein (TBP), component of	99.97
PRK00394	179	transcription factor; Reviewed	99.96
cd04518	174	TBP_archaea archaeal TATA box binding protein (TBP	99.96
cd00652	174	TBP_TLF TATA box binding protein (TBP): Present in	99.94
cd04516	174	TBP_eukaryotes eukaryotic TATA box binding protein	99.94
PLN00062	179	TATA-box-binding protein; Provisional	99.94
cd04517	174	TLF TBP-like factors (TLF; also called TLP, TRF, T	99.93
KOG3302	200	consensus TATA-box binding protein (TBP), componen	99.86
PF11858	81	DUF3378: Domain of unknown function (DUF3378); Int	97.13
PF11858	81	DUF3378: Domain of unknown function (DUF3378); Int	96.76
COG4871	193	Uncharacterized protein conserved in archaea [Func	96.63
TIGR00716	284	rnhC ribonuclease HIII. Two types of ribonuclease	95.06
COG1039	297	RnhC Ribonuclease HIII [DNA replication, recombina	94.46
COG1039	297	RnhC Ribonuclease HIII [DNA replication, recombina	94.41
PRK00996	304	ribonuclease HIII; Provisional	94.37
COG4871	193	Uncharacterized protein conserved in archaea [Func	93.77
PRK00996	304	ribonuclease HIII; Provisional	93.72
TIGR00716	284	rnhC ribonuclease HIII. Two types of ribonuclease	93.12
PRK12475	338	thiamine/molybdopterin biosynthesis MoeB-like prot	89.49
PRK07688	339	thiamine/molybdopterin biosynthesis ThiF/MoeB-like	86.17
TIGR02187	215	GlrX_arch Glutaredoxin-like domain protein. This f	81.34

>PLN00062 TATA-box-binding protein; Provisional

Probab=100.00  E-value=1.9e-70  Score=439.74  Aligned_cols=179  Identities=74%  Similarity=1.203  Sum_probs=175.8

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      +|+|+|||||+++++++||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
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            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239           82 QKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI  161 (180)
Q Consensus        82 ~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~  161 (180)
                      +++|+++++.+|+|+|||||+|++|+|||++||..|.++++||||+||||+||+.+|++|++||+||||+|||+|+++|+
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            99999999999999999999999999999999988899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCC
Q 047239          162 YAAFNNIYPVLNVYVTYDQ  180 (180)
Q Consensus       162 ~~a~~~i~~~L~~~~~~~~  180 (180)
                      ++|++.|+|+|.+|++.+|
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=1.1e-69  Score=433.76  Aligned_cols=174  Identities=75%  Similarity=1.217  Sum_probs=171.3

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      +|+|+|||||++++|++||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+|+++.|+++++++|
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            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239           82 QKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI  161 (180)
Q Consensus        82 ~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~  161 (180)
                      +++|+++++.+|+|+|||||+|++|+|||++||..|.++++||||+||||+||+.+|+++++||+||||+|||+|+++|+
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            99999999999999999999999999999999988889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhc
Q 047239          162 YAAFNNIYPVLNVY  175 (180)
Q Consensus       162 ~~a~~~i~~~L~~~  175 (180)
                      ++|+++|+|+|.+|
T Consensus       161 ~~a~~~i~p~L~~~  174 (174)
T cd04516         161 YQAFENIYPILLQF  174 (174)
T ss_pred             HHHHHHHHHHHhhC
Confidence            99999999999986

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.

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

Probab=100.00  E-value=4.7e-68  Score=424.04  Aligned_cols=180  Identities=69%  Similarity=1.132  Sum_probs=176.5

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      +.+.++||||+++++|++||.+||...+|++|||++|++++||+++|++|++||+||||+||||+|+++++.|+++++++
T Consensus        21 i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~aRi  100 (200)
T KOG3302|consen   21 LDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYARI  100 (200)
T ss_pred             cceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           81 VQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        81 L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      ||++|+++++.||++|||+||||++|+|+||+++..|+.+++||||+||||+|||.+|+++++||+||||++|||++.+|
T Consensus       101 lqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~  180 (200)
T KOG3302|consen  101 LQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREE  180 (200)
T ss_pred             HHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccCC
Q 047239          161 IYAAFNNIYPVLNVYVTYDQ  180 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~~~~  180 (180)
                      +.+|+++|||+|.+||+.-+
T Consensus       181 i~~Ai~~IyPil~~frk~~~  200 (200)
T KOG3302|consen  181 TYEAIENIYPILLEFRKKLL  200 (200)
T ss_pred             HHHHHHHHhHHHHHhhhccC
Confidence            99999999999999998643

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

Probab=100.00  E-value=2.3e-67  Score=414.07  Aligned_cols=176  Identities=43%  Similarity=0.677  Sum_probs=170.2

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      ++++|+|||||++|++++||+.++..+++++|||++||||+||+++||+++|||+|||+|||||||.+|++.|+++++++
T Consensus         6 ~~i~IeNIVAS~~L~~elDL~~~~~~l~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~~~   85 (185)
T COG2101           6 PTITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLAKK   85 (185)
T ss_pred             CccEEEEEEEEechhhhccHHHHHhhCCCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCccc-ceeeeeeEEEEecCcccchhhHhhh-cCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCH
Q 047239           81 VQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLERLNGF-HAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAR  158 (180)
Q Consensus        81 L~~~g~~~~~~-~~~i~NIva~~~~~~~i~L~~la~~-~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~  158 (180)
                      |++.|+++.+. .++|||||||+|++.++||+.+|.. ..++++|||||||||+||+.+|++++|||.|||+||||||++
T Consensus        86 L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~  165 (185)
T COG2101          86 LKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSE  165 (185)
T ss_pred             HHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCH
Confidence            99999999987 7999999999999999999999987 445699999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcc
Q 047239          159 EQIYAAFNNIYPVLNVYV  176 (180)
Q Consensus       159 ~~~~~a~~~i~~~L~~~~  176 (180)
                      +|+++|+++|++.|.++.
T Consensus       166 ed~~~Av~~i~~~L~elg  183 (185)
T COG2101         166 EDAEQAVEKIQSRLEELG  183 (185)
T ss_pred             HHHHHHHHHHHHHHHHhc
Confidence            999999999999998875

>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=3e-66  Score=414.22  Aligned_cols=173  Identities=70%  Similarity=1.120  Sum_probs=168.7

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||++++++++||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
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            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCC-cccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           82 QKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        82 ~~~g~~~-~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      +++|++. ++.+|+|+|||||++++|+|||++||..+.++++||||+||||+||+.+|++|++||+||||+|||+|+++|
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            9999987 888999999999999999999999998877899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 047239          161 IYAAFNNIYPVLNV  174 (180)
Q Consensus       161 ~~~a~~~i~~~L~~  174 (180)
                      +++|+++|+|+|.+
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

>PRK00394 transcription factor; Reviewed

Probab=100.00  E-value=5.4e-66  Score=414.28  Aligned_cols=175  Identities=42%  Similarity=0.626  Sum_probs=169.0

Q ss_pred             ceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHH
Q 047239            3 PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQ   82 (180)
Q Consensus         3 ~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~   82 (180)
                      ++|+|||||++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|+
T Consensus         1 i~i~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l~   80 (179)
T PRK00394          1 IKIENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKLK   80 (179)
T ss_pred             CEEEEEEEEEEcCCCcCHHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHHH
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HcCCCCc-ccceeeeeeEEEEecCcccchhhHhhh-cCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           83 KIGFPVQ-FKDFKIQNIVGSCDVEFPIKLERLNGF-HAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        83 ~~g~~~~-~~~~~i~NIva~~~~~~~i~L~~la~~-~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      ++|+++. ..+|+|+|||||++++++|||++++.. +.++++||||+||||+||+.+|++|++||+||||+||||||++|
T Consensus        81 ~~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~  160 (179)
T PRK00394         81 ELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEED  160 (179)
T ss_pred             HcCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence            9999886 679999999999999999999999986 34899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccc
Q 047239          161 IYAAFNNIYPVLNVYVT  177 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~  177 (180)
                      +++|+++|+|+|.++..
T Consensus       161 ~~~a~~~i~~~l~~~g~  177 (179)
T PRK00394        161 AEKAVEKILEKLEELGL  177 (179)
T ss_pred             HHHHHHHHHHHHHHcCC
Confidence            99999999999998764

>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=1e-65  Score=410.91  Aligned_cols=173  Identities=42%  Similarity=0.667  Sum_probs=166.9

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      +++|+|||||++++++|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
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            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCCc-ccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           82 QKIGFPVQ-FKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        82 ~~~g~~~~-~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      +++|++.. ..+|+|+|||||++++++|||+.|+.. .++++||||+||||+||+.+|++|++||+||||+||||||++|
T Consensus        81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~-~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~  159 (174)
T cd04518          81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIG-LPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEED  159 (174)
T ss_pred             HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhh-CCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHH
Confidence            99999875 458999999999999999999999986 4599999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhc
Q 047239          161 IYAAFNNIYPVLNVY  175 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~  175 (180)
                      ++.|+++|+|+|.++
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.

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

Probab=100.00  E-value=3e-65  Score=408.42  Aligned_cols=172  Identities=46%  Similarity=0.855  Sum_probs=168.2

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||++++++++||+++|..++|++||| +|||++||+++|+++++||+|||++|||++|+++++.|++++.++|
T Consensus         2 ~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l   80 (174)
T cd04517           2 DILIVNVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLL   80 (174)
T ss_pred             ccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999 9999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCC-cccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           82 QKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        82 ~~~g~~~-~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      +++|++. ++.+|+|+|||||++++|+|||++|+..|.++++||||+||||+||+.+|++|++||+||||+|||+|+++|
T Consensus        81 ~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~  160 (174)
T cd04517          81 QKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMED  160 (174)
T ss_pred             HHcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHH
Confidence            9999987 889999999999999999999999998888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 047239          161 IYAAFNNIYPVLNV  174 (180)
Q Consensus       161 ~~~a~~~i~~~L~~  174 (180)
                      +++|+++|+|+|.+
T Consensus       161 ~~~a~~~i~pil~~  174 (174)
T cd04517         161 VREAVEKIYPIVFE  174 (174)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999999974

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=99.97  E-value=1e-31  Score=192.00  Aligned_cols=84  Identities=50%  Similarity=0.724  Sum_probs=80.2

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||+++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|++++.++|
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            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcC
Q 047239           82 QKIG   85 (180)
Q Consensus        82 ~~~g   85 (180)
                      +++|
T Consensus        83 ~~~~   86 (86)
T PF00352_consen   83 QKLG   86 (86)
T ss_dssp             HHTT
T ss_pred             HHcC
Confidence            9986

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 ....

>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=99.97  E-value=7.2e-32  Score=192.78  Aligned_cols=86  Identities=52%  Similarity=0.804  Sum_probs=80.5

Q ss_pred             ccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHH
Q 047239           90 FKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIY  169 (180)
Q Consensus        90 ~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~  169 (180)
                      |.+++|+||||+++++++|||++|+.. .++++||||+|||++||+.+|++|++||+||||+||||+|+++++.|+++++
T Consensus         1 ~~~~~i~NIva~~~l~~~idL~~la~~-~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~   79 (86)
T PF00352_consen    1 FPDFKIVNIVASFDLPFEIDLEELAEE-LENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKIL   79 (86)
T ss_dssp             -EEEEEEEEEEEEE-SSEB-HHHHHHH-STTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred             CCccEEEEEEEEEECCCccCHHHHHhh-ccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHH
Confidence            568999999999999999999999987 5999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcc
Q 047239          170 PVLNVYV  176 (180)
Q Consensus       170 ~~L~~~~  176 (180)
                      |+|.+|+
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 ....

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

Probab=99.97  E-value=1.5e-30  Score=205.48  Aligned_cols=85  Identities=39%  Similarity=0.629  Sum_probs=81.3

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCC--cEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARN--AEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYAR   79 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n--~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~   79 (180)
                      .++|||||||+|++.++||+.+|..+++  ++|||||||||+||+.+|++.+|||+|||+||||||+++|++.|++++.+
T Consensus        98 ~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~  177 (185)
T COG2101          98 EIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQS  177 (185)
T ss_pred             ceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHHHH
Confidence            4789999999999999999999987655  99999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCC
Q 047239           80 IVQKIGF   86 (180)
Q Consensus        80 ~L~~~g~   86 (180)
                      .|+++|.
T Consensus       178 ~L~elgl  184 (185)
T COG2101         178 RLEELGL  184 (185)
T ss_pred             HHHHhcc
Confidence            9999874

>PRK00394 transcription factor; Reviewed

Probab=99.96  E-value=1.9e-29  Score=202.64  Aligned_cols=85  Identities=40%  Similarity=0.662  Sum_probs=82.6

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhC--CCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHA--RNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYAR   79 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~--~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~   79 (180)
                      .++|+|||||++++++|||+.+|..+  +|++||||+||||+||+.+|+++++||+||||+||||||++|++.|++++.+
T Consensus        91 ~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~  170 (179)
T PRK00394         91 EIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKILE  170 (179)
T ss_pred             ceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHH
Confidence            57999999999999999999999887  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCC
Q 047239           80 IVQKIGF   86 (180)
Q Consensus        80 ~L~~~g~   86 (180)
                      +|+++|.
T Consensus       171 ~l~~~g~  177 (179)
T PRK00394        171 KLEELGL  177 (179)
T ss_pred             HHHHcCC
Confidence            9999985

>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=99.96  E-value=5.1e-29  Score=199.34  Aligned_cols=83  Identities=43%  Similarity=0.643  Sum_probs=80.5

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+|||||++++++|||+.+|..++|++||||+||||+||+.+|+++++||+||||+||||||++|++.|++++.++|
T Consensus        92 ~~~i~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~~l  171 (174)
T cd04518          92 EIKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLSRL  171 (174)
T ss_pred             ceEEEEEEEEEEcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHc
Q 047239           82 QKI   84 (180)
Q Consensus        82 ~~~   84 (180)
                      +++
T Consensus       172 ~~~  174 (174)
T cd04518         172 KEL  174 (174)
T ss_pred             hhC
Confidence            863

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.

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

Probab=99.94  E-value=3.7e-27  Score=188.62  Aligned_cols=81  Identities=42%  Similarity=0.578  Sum_probs=78.5

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCC-CcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHAR-NAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~-n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      .++|+||||+++++++|||+.||...+ +++||||+||||+||+.+|++|++||+||||+|||+||++|++.|++++.++
T Consensus        92 ~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~  171 (174)
T cd00652          92 EFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPI  171 (174)
T ss_pred             ceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHH
Confidence            579999999999999999999999885 9999999999999999999999999999999999999999999999999999


Q ss_pred             HH
Q 047239           81 VQ   82 (180)
Q Consensus        81 L~   82 (180)
                      |.
T Consensus       172 L~  173 (174)
T cd00652         172 LK  173 (174)
T ss_pred             Hh
Confidence            86

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

>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=99.94  E-value=4.2e-27  Score=188.30  Aligned_cols=83  Identities=33%  Similarity=0.476  Sum_probs=79.4

Q ss_pred             eeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHHH
Q 047239           93 FKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL  172 (180)
Q Consensus        93 ~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L  172 (180)
                      ++|+|||||++++++|||++|+.. .++++||||+||||+||+.+|++|++||+||||+||||+|.++++.|+++++++|
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 PKIQNIVATVNLGCKLDLKKIALR-ARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII   80 (174)
T ss_pred             CEEEEEEEEEEcCCeecHHHHHhh-CCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence            589999999999999999999975 7889999999999999999999999999999999999999999999999999999


Q ss_pred             hhcc
Q 047239          173 NVYV  176 (180)
Q Consensus       173 ~~~~  176 (180)
                      .++-
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=99.94  E-value=1e-26  Score=186.75  Aligned_cols=84  Identities=33%  Similarity=0.496  Sum_probs=80.7

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHh-hCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIAL-HARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~-~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      .++|+|||||+|++++|||+.||. +.++++||||+||||+||+.+|+++++||+||||++||+||++|++.|++++.++
T Consensus        91 ~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~ai~~i~p~  170 (179)
T PLN00062         91 DFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYPV  170 (179)
T ss_pred             ccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHH
Confidence            579999999999999999999996 4689999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcC
Q 047239           81 VQKIG   85 (180)
Q Consensus        81 L~~~g   85 (180)
                      |.+++
T Consensus       171 L~~~~  175 (179)
T PLN00062        171 LTEFR  175 (179)
T ss_pred             HHHhc
Confidence            99876

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

Probab=99.93  E-value=1e-25  Score=180.31  Aligned_cols=81  Identities=31%  Similarity=0.449  Sum_probs=77.8

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhh-CCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALH-ARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~-~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      .++|+||||+++++++|||+.+|.. .++++||||+|||++||+.+|+++++||+||||+|||+||++|++.|++++.++
T Consensus        92 ~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pi  171 (174)
T cd04517          92 NFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPI  171 (174)
T ss_pred             ceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHH
Confidence            5799999999999999999999975 589999999999999999999999999999999999999999999999999998


Q ss_pred             HH
Q 047239           81 VQ   82 (180)
Q Consensus        81 L~   82 (180)
                      |.
T Consensus       172 l~  173 (174)
T cd04517         172 VF  173 (174)
T ss_pred             Hh
Confidence            85

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=1.7e-21  Score=156.44  Aligned_cols=85  Identities=29%  Similarity=0.443  Sum_probs=80.4

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhh-CCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALH-ARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYAR   79 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~-~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~   79 (180)
                      +.++|+||+||+|+.++|+|+.++.. ...+.||||.||||+||+.+|+++++||.||||++|||++.++.++|+++|.+
T Consensus       111 ~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~i~~Ai~~IyP  190 (200)
T KOG3302|consen  111 RDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREETYEAIENIYP  190 (200)
T ss_pred             hheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHHHHHHHHHHhH
Confidence            36899999999999999999999975 57899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcC
Q 047239           80 IVQKIG   85 (180)
Q Consensus        80 ~L~~~g   85 (180)
                      +|.++.
T Consensus       191 il~~fr  196 (200)
T KOG3302|consen  191 ILLEFR  196 (200)
T ss_pred             HHHHhh
Confidence            998763

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

Probab=97.13  E-value=0.00061  Score=48.22  Aligned_cols=36  Identities=28%  Similarity=0.360  Sum_probs=30.2

Q ss_pred             CccceEEEEecCCcEEEEEecCCcEEEEccCCHHHH
Q 047239           35 SRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQA   70 (180)
Q Consensus        35 e~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~   70 (180)
                      ..=|+.+++.+.+.+++++|.|||++..|...+..|
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            344899999999999999999999999999655555

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.

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

Probab=96.76  E-value=0.0016  Score=46.08  Aligned_cols=36  Identities=31%  Similarity=0.444  Sum_probs=29.6

Q ss_pred             cCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239          126 ELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI  161 (180)
Q Consensus       126 e~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~  161 (180)
                      ..=||..|+...+.+|+.+|.||||++.|...+.++
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            334899999999999999999999999999654433

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=96.63  E-value=0.016  Score=46.25  Aligned_cols=62  Identities=23%  Similarity=0.269  Sum_probs=52.5

Q ss_pred             CHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHH
Q 047239           19 DLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQK   83 (180)
Q Consensus        19 dL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~   83 (180)
                      -|.-||..++++.|..++ ..++++.-  ..-+.||.|||+..|-.|++++|++++..+.+++++
T Consensus        47 ilplla~l~P~anY~~kk-~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ine  108 (193)
T COG4871          47 ILPLLAPLFPRANYSDKK-NILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE  108 (193)
T ss_pred             hHHHhHhhCCCccccccc-ceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence            356678888999999765 67777754  456789999999999999999999999999998886

>TIGR00716 rnhC ribonuclease HIII

Probab=95.06  E-value=0.047  Score=47.03  Aligned_cols=36  Identities=22%  Similarity=0.385  Sum_probs=30.3

Q ss_pred             cCCccceEEEEecCCcEEEEEecCCcEEEEccCCHH
Q 047239           33 NPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSES   68 (180)
Q Consensus        33 ePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~   68 (180)
                      .+..=|+.+|+.+.|.+|+.+|.|||++..|...++
T Consensus        22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~ae~   57 (284)
T TIGR00716        22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNSEK   57 (284)
T ss_pred             ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCHHH
Confidence            445568999999999999999999999999954433

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.

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

Probab=94.46  E-value=0.1  Score=45.16  Aligned_cols=41  Identities=37%  Similarity=0.455  Sum_probs=35.7

Q ss_pred             cCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239          126 ELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFN  166 (180)
Q Consensus       126 e~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~  166 (180)
                      ..-|+.+|+...|.+|+.+|.|||+++.|-..++.+++-..
T Consensus        27 ~~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~   67 (297)
T COG1039          27 SNPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLN   67 (297)
T ss_pred             cCCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhh
Confidence            37789999999999999999999999999987776666554

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

Probab=94.41  E-value=0.11  Score=45.01  Aligned_cols=43  Identities=30%  Similarity=0.325  Sum_probs=37.1

Q ss_pred             ccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHH
Q 047239           36 RFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYA   78 (180)
Q Consensus        36 ~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~   78 (180)
                      ..|+.+|+.+.|.+|+.+|.|||+++.|-.+++-+++-...+.
T Consensus        28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~   70 (297)
T COG1039          28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIA   70 (297)
T ss_pred             CCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhh
Confidence            6789999999999999999999999999988777776666443

>PRK00996 ribonuclease HIII; Provisional

Probab=94.37  E-value=0.081  Score=45.99  Aligned_cols=35  Identities=31%  Similarity=0.470  Sum_probs=29.6

Q ss_pred             CCccceEEEEecCCcEEEEEecCCcEEEEccCCHH
Q 047239           34 PSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSES   68 (180)
Q Consensus        34 Pe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~   68 (180)
                      +..-|+..|+.+.+.+++.+|.|||+++.|...++
T Consensus        26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae~   60 (304)
T PRK00996         26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAEA   60 (304)
T ss_pred             cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHHH
Confidence            34567999999999999999999999999964433

>COG4871 Uncharacterized protein conserved in archaea [Function unknown]

Probab=93.77  E-value=0.51  Score=37.75  Aligned_cols=73  Identities=19%  Similarity=0.193  Sum_probs=55.3

Q ss_pred             eEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239           98 IVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNV  174 (180)
Q Consensus        98 Iva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~  174 (180)
                      +.+..+-+++=-|..|+.- .+++.|.- .-.-|+++.-  ..-+.|+.||||.+|--++++++++++..+..++.+
T Consensus        36 Vi~~md~~lg~ilplla~l-~P~anY~~-kk~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ine  108 (193)
T COG4871          36 VIANMDPPLGGILPLLAPL-FPRANYSD-KKNILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE  108 (193)
T ss_pred             EEeecCCCcchhHHHhHhh-CCCccccc-ccceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence            3555565665556667654 55688884 4566777644  456789999999999999999999999999988875

>PRK00996 ribonuclease HIII; Provisional

Probab=93.72  E-value=0.13  Score=44.80  Aligned_cols=35  Identities=46%  Similarity=0.754  Sum_probs=30.2

Q ss_pred             CCcCCceeEEEecCCeEEEEEecCceEEEEcccCH
Q 047239          124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAR  158 (180)
Q Consensus       124 ePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~  158 (180)
                      .+..-|+..|+...+.+|+.+|.||||++.|...+
T Consensus        25 ~~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae   59 (304)
T PRK00996         25 TPSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE   59 (304)
T ss_pred             ccCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence            34556899999999999999999999999996543

>TIGR00716 rnhC ribonuclease HIII

Probab=93.12  E-value=0.17  Score=43.55  Aligned_cols=34  Identities=24%  Similarity=0.490  Sum_probs=29.9

Q ss_pred             CCcCCceeEEEecCCeEEEEEecCceEEEEcccC
Q 047239          124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKA  157 (180)
Q Consensus       124 ePe~fpgli~r~~~p~~t~lIF~sGkivitGaks  157 (180)
                      ++..=||..|+...+.+|+.+|.||||++.|...
T Consensus        22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~a   55 (284)
T TIGR00716        22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNS   55 (284)
T ss_pred             ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCH
Confidence            4556799999999999999999999999999543

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=89.49  E-value=1.7  Score=38.17  Aligned_cols=60  Identities=15%  Similarity=0.354  Sum_probs=43.2

Q ss_pred             CccCHHHHHhhCC-CcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHH
Q 047239           16 CKLDLKKIALHAR-NAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYA   78 (180)
Q Consensus        16 ~~ldL~~la~~~~-n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~   78 (180)
                      ..+|+++++..+. -..++...| .+.++..  .-.+.+|+.|++.+.|++++.+|+.-..++.
T Consensus       277 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~f~~gr~~~~g~~~~~~a~~~~~~~~  337 (338)
T PRK12475        277 RRLNLEEIKKRLQKIGKVDANPY-LLSFQLD--EYRFVLFTDGRAFIHGTNDIKKAKRLYARYI  337 (338)
T ss_pred             CccCHHHHHHHHhhcCEEEeccc-EEEEEEC--CEEEEEEcCCcEEEECCCCHHHHHHHHHHhc
Confidence            5899999987653 123332222 3456554  4688899999999999999999988777653

>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated

Probab=86.17  E-value=2.4  Score=37.33  Aligned_cols=59  Identities=22%  Similarity=0.387  Sum_probs=44.4

Q ss_pred             CccCHHHHHhhCCCc--EEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHH
Q 047239           16 CKLDLKKIALHARNA--EYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKY   77 (180)
Q Consensus        16 ~~ldL~~la~~~~n~--~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i   77 (180)
                      ..+++++++..+...  ++..   +.+.++++.+.-.+..|++|++++.|++++..|+.-..++
T Consensus       277 ~~i~~~~~~~~l~~~~~~~~~---~~~ll~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~  337 (339)
T PRK07688        277 EEYDLEELAELLRDRGLDVNV---NPYLLSFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRY  337 (339)
T ss_pred             CccCHHHHHHHHHhcccccCC---CcEEEEEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence            468888888776432  3433   3345566666689999999999999999999998877665

>TIGR02187 GlrX_arch Glutaredoxin-like domain protein

Probab=81.34  E-value=14  Score=29.85  Aligned_cols=115  Identities=17%  Similarity=0.114  Sum_probs=65.3

Q ss_pred             EEEEEecCCcEE---EEccCCHHHHHHHHHHHHHHHHHcCCCCcc---------c-ceeeeeeEEEEecCccc---chhh
Q 047239           49 TTALIFSSGKIV---CTGAKSESQAKLAARKYARIVQKIGFPVQF---------K-DFKIQNIVGSCDVEFPI---KLER  112 (180)
Q Consensus        49 ~t~lIf~SGKiv---itGaks~~~~~~a~~~i~~~L~~~g~~~~~---------~-~~~i~NIva~~~~~~~i---~L~~  112 (180)
                      -|+.+|.+|+.+   ..|..+.+++..-++.+... ..-+.....         . ...|.-..+..+-+|+.   -+++
T Consensus        79 Pt~~~f~~g~~~~~~~~G~~~~~~l~~~i~~~~~~-~~~~~~L~~~~~~~l~~~~~pv~I~~F~a~~C~~C~~~~~~l~~  157 (215)
T TIGR02187        79 PTTIILEEGKDGGIRYTGIPAGYEFAALIEDIVRV-SQGEPGLSEKTVELLQSLDEPVRIEVFVTPTCPYCPYAVLMAHK  157 (215)
T ss_pred             CEEEEEeCCeeeEEEEeecCCHHHHHHHHHHHHHh-cCCCCCCCHHHHHHHHhcCCCcEEEEEECCCCCCcHHHHHHHHH
Confidence            388999999886   47998888876666655422 211111111         1 12333334554444441   2444


Q ss_pred             HhhhcC--CCCccCCcCCceeE--EEecCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239          113 LNGFHA--MFSTYEPELFPGLI--YRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFN  166 (180)
Q Consensus       113 la~~~~--~~~~YePe~fpgli--~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~  166 (180)
                      ++..+.  ....+|++.+|.+.  |.+.. --|+.+|..|+. +.|..+.+++.+.+.
T Consensus       158 l~~~~~~i~~~~vD~~~~~~~~~~~~V~~-vPtl~i~~~~~~-~~G~~~~~~l~~~l~  213 (215)
T TIGR02187       158 FALANDKILGEMIEANENPDLAEKYGVMS-VPKIVINKGVEE-FVGAYPEEQFLEYIL  213 (215)
T ss_pred             HHHhcCceEEEEEeCCCCHHHHHHhCCcc-CCEEEEecCCEE-EECCCCHHHHHHHHH
Confidence            443321  12346777777764  33322 236778888875 889999888777664

This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	180
1vok_A	200	Arabidopsis Thaliana Tbp (Dimer) Length = 200		1e-75
1vtl_E	186	Co-Crystal Structure Of Tbp Recognizing The Minor G		1e-75
1vto_A	190	1.9 A Resolution Refined Structure Of Tbp Recognizi		1e-75
1jfi_C	185	Crystal Structure Of The Nc2-Tbp-Dna Ternary Comple		7e-74
1tgh_A	185	Tata Binding Protein (Tbp)DNA COMPLEX Length = 185		8e-74
1nvp_A	181	Human TfiiaTBPDNA COMPLEX Length = 181		8e-74
1c9b_B	180	Crystal Structure Of A Human Tbp Core Domain-Human		1e-73
1cdw_A	179	Human Tbp Core Domain Complexed With Dna Length = 1		5e-73
1rm1_A	240	Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex L		5e-73
1ytb_A	180	Crystal Structure Of A Yeast TbpTATA-Box Complex Le		9e-73
1tbp_A	180	Crystal Structure Of Yeast Tata-Binding Protein And		9e-73
3oc3_C	218	Crystal Structure Of The Mot1 N-Terminal Domain In		9e-68
3eik_A	218	Double Stranded Dna Binding Protein Length = 218		9e-68
1mp9_A	198	Tbp From A Mesothermophilic Archaeon, Sulfolobus Ac		2e-32
1mp9_A	198	Tbp From A Mesothermophilic Archaeon, Sulfolobus Ac		1e-09
2z8u_A	188	Methanococcus Jannaschii Tbp Length = 188		1e-29
1ais_A	182	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-		2e-27
1d3u_A	181	Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+T		2e-27
1pcz_A	191	Structure Of Tata-Binding Protein Length = 191		2e-27

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

Iteration: 1
 Score =  278 bits (711), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 154/180 (85%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 21  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 80
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE  +K+AARKYARIVQK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   HA F
Sbjct: 81  CTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAF 140
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK P + +LIF+SGK+VITGAK R++ Y AF NIYPVL+ +    Q
Sbjct: 141 SSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQQ 200

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

Iteration: 1
 Score =  278 bits (710), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 129/175 (73%), Positives = 153/175 (87%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 9   IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 68
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE  +K+AARKYARIVQK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   HA F
Sbjct: 69  CTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAF 128
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRMK P + +LIF+SGK+VITGAK R++ Y AF NIYPVL+ +
Sbjct: 129 SSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEF 183

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

Iteration: 1
 Score =  278 bits (710), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 130/180 (72%), Positives = 154/180 (85%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 11  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 70
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE  +K+AARKYARIVQK+GFP +FKDFKIQNIVGSCDV+FPI+LE L   HA F
Sbjct: 71  CTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAF 130
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ 180
           S+YEPELFPGLIYRMK P + +LIF+SGK+VITGAK R++ Y AF NIYPVL+ +    Q
Sbjct: 131 SSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQQ 190

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

Iteration: 1
 Score =  272 bits (696), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 126/175 (72%), Positives = 150/175 (85%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct: 7   IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 66
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct: 67  CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 126
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L  +
Sbjct: 127 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGF 181

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

Iteration: 1
 Score =  272 bits (695), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 126/175 (72%), Positives = 150/175 (85%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct: 7   IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 66
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct: 67  CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 126
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L  +
Sbjct: 127 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGF 181

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

Iteration: 1
 Score =  272 bits (695), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 126/172 (73%), Positives = 149/172 (86%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct: 3   IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 62
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct: 63  CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 122
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct: 123 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPIL 174

>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 =  272 bits (695), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 126/175 (72%), Positives = 150/175 (85%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct: 4   IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 63
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE Q++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct: 64  CTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 123
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L  +
Sbjct: 124 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGF 178

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

Iteration: 1
 Score =  269 bits (688), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 125/172 (72%), Positives = 148/172 (86%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIV+T+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EP+TTALIFSSGK+V
Sbjct: 3   IVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMV 62
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
           CTGAKSE  ++LAARKYAR+VQK+GFP +F DFKIQN+VGSCDV+FPI+LE L   H  F
Sbjct: 63  CTGAKSEENSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQF 122
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           S+YEPELFPGLIYRM KP + +LIF+SGKVV+TGAK R +IY AF NIYP+L
Sbjct: 123 SSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPIL 174

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

Iteration: 1
 Score =  269 bits (688), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 124/175 (70%), Positives = 148/175 (84%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIVAT+ L C+LDLK +ALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 63  IVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 122
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
            TGAKSE  +KLA+RKYARI+QKIGF  +F DFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 123 VTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTF 182
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK RE+IY AF  IYPVL+ +
Sbjct: 183 SSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEF 237

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

Iteration: 1
 Score =  268 bits (686), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 124/175 (70%), Positives = 148/175 (84%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIVAT+ L C+LDLK +ALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 3   IVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 62
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
            TGAKSE  +KLA+RKYARI+QKIGF  +F DFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 63  VTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTF 122
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK RE+IY AF  IYPVL+ +
Sbjct: 123 SSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEF 177

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

Iteration: 1
 Score =  268 bits (686), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 124/175 (70%), Positives = 148/175 (84%)
Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIVAT+ L C+LDLK +ALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 3   IVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 62
Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
            TGAKSE  +KLA+RKYARI+QKIGF  +F DFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 63  VTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTF 122
Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK RE+IY AF  IYPVL+ +
Sbjct: 123 SSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEF 177

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

Iteration: 1
 Score =  252 bits (643), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 115/170 (67%), Positives = 142/170 (83%)
Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QN+VAT+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V T
Sbjct: 43  PTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVIT 102
Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE  +++AA++YA+I+ K+GF   F DFKIQNIV SCD++F I+LE L   H+ + +
Sbjct: 103 GAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSNYCS 162
Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK R+ IY AFNNIYPVL
Sbjct: 163 YEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVL 212

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

Iteration: 1
 Score =  252 bits (643), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 115/170 (67%), Positives = 142/170 (83%)
Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QN+VAT+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V T
Sbjct: 43  PTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVIT 102
Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE  +++AA++YA+I+ K+GF   F DFKIQNIV SCD++F I+LE L   H+ + +
Sbjct: 103 GAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSNYCS 162
Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
           YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK R+ IY AFNNIYPVL
Sbjct: 163 YEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVL 212

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

Iteration: 1
 Score =  134 bits (338), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 71/166 (42%), Positives = 104/166 (62%), Gaps = 2/166 (1%)
Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I+NIVAT+ L+  LDL  +     N EY+P +F  +  R++ PK T+LIF SGK+V TGA
Sbjct: 15  IENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGA 74
Query: 65  KSESQAKLAARKYARIVQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTY 123
           KS  +   A ++  + ++K G  +  K   +IQNIV S ++   + L++   F    + Y
Sbjct: 75  KSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDK-AAFLLENNMY 133
Query: 124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIY 169
           EPE FPGLIYRM +P V +LIF SGK+VITGAK  ++++ A   I+
Sbjct: 134 EPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIF 179

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 51/86 (59%), Gaps = 11/86 (12%)
Query: 95  IQNIVGSCDVEFPIKLERLNGFHAMFST-----YEPELFPGLIYRMKKPNVTMLIFLSGK 149
           I+NIV +      + L++    +AM  +     Y+P+ FPGLI+R++ P +T LIF SGK
Sbjct: 15  IENIVAT------VTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGK 68
Query: 150 VVITGAKAREQIYAAFNNIYPVLNVY 175
           +V+TGAK+ +++  A   I   L  Y
Sbjct: 69  MVVTGAKSTDELIKAVKRIIKTLKKY 94

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

Iteration: 1
 Score =  125 bits (315), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 68/171 (39%), Positives = 101/171 (59%), Gaps = 4/171 (2%)
Query: 1   MAPVIQ--NIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGK 58
           M P I+  N+V +  +   +DL+++A+   NAEY P +F  +  R+  PK   LIF SGK
Sbjct: 9   MEPEIKIVNVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGK 68
Query: 59  IVCTGAKSESQAKLAARKYARIVQKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFH 117
           + CTGAKS+ +A++A +K  + ++  G  V +  + KIQN+V + D+     L+ +    
Sbjct: 69  VNCTGAKSKEEAEIAIKKIIKELKDAGIDVIENPEIKIQNMVATADLGIEPNLDDI-ALM 127
Query: 118 AMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNI 168
              + YEPE FPGL+YR+  P V +LIF SGKVVITG K+ E    A   I
Sbjct: 128 VEGTEYEPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKI 178

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

Iteration: 1
 Score =  118 bits (296), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 70/177 (39%), Positives = 106/177 (59%), Gaps = 10/177 (5%)
Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I+NIVA+++L  +LDL+K+     N++YNP  F  +   + +PK   LIFSSGK+V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 65  KSESQAKLAARKYARIVQKIGFPVQFK---DFKIQNIVGSCDV--EFPIKLERLNGFHAM 119
           KS    + A  K A+ ++ IG  V+FK      +QN+V S D+  EF + +  L   +  
Sbjct: 71  KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNC- 127
Query: 120 FSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYV 176
              YEPE FPG+IYR+K+P   +L+F SGK+V +GAK+    + A   +   L+ Y+
Sbjct: 128 --EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKYL 182

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

Iteration: 1
 Score =  118 bits (295), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 70/176 (39%), Positives = 105/176 (59%), Gaps = 10/176 (5%)
Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I+NIVA+++L  +LDL+K+     N++YNP  F  +   + +PK   LIFSSGK+V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 65  KSESQAKLAARKYARIVQKIGFPVQFK---DFKIQNIVGSCDV--EFPIKLERLNGFHAM 119
           KS    + A  K A+ ++ IG  V+FK      +QN+V S D+  EF + +  L   +  
Sbjct: 71  KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNC- 127
Query: 120 FSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
              YEPE FPG+IYR+K+P   +L+F SGK+V +GAK+    + A   +   L+ Y
Sbjct: 128 --EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181

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

Iteration: 1
 Score =  118 bits (295), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 70/176 (39%), Positives = 105/176 (59%), Gaps = 10/176 (5%)
Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I+NIVA+++L  +LDL+K+     N++YNP  F  +   + +PK   LIFSSGK+V TGA
Sbjct: 11  IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 65  KSESQAKLAARKYARIVQKIGFPVQFK---DFKIQNIVGSCDV--EFPIKLERLNGFHAM 119
           KS    + A  K A+ ++ IG  V+FK      +QN+V S D+  EF + +  L   +  
Sbjct: 71  KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNC- 127
Query: 120 FSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
              YEPE FPG+IYR+K+P   +L+F SGK+V +GAK+    + A   +   L+ Y
Sbjct: 128 --EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	180
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	4e-76
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	2e-19
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	3e-73
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	2e-24
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	7e-72
1ytb_A	180	Protein (tata binding protein (TBP)); protein-DNA	1e-71
1mp9_A	198	Tata-binding protein; transcription regulation, DN	3e-71
1mp9_A	198	Tata-binding protein; transcription regulation, DN	3e-23
1mp9_A	198	Tata-binding protein; transcription regulation, DN	1e-17
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	1e-69
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	1e-17

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

 Score =  226 bits (576), Expect = 4e-76
 Identities = 115/173 (66%), Positives = 143/173 (82%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QN+VAT+NL CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V T
Sbjct: 43  PTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVIT 102

Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE  +++AA++YA+I+ K+GF   F DFKIQNIV SCD++F I+LE L   H+ + +
Sbjct: 103 GAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSNYCS 162

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK R+ IY AFNNIYPVL  +
Sbjct: 163 YEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVLIQH 215

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

 Score = 80.9 bits (199), Expect = 2e-19
 Identities = 29/118 (24%), Positives = 53/118 (44%), Gaps = 2/118 (1%)

Query: 56  SGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLERLN 114
                 +G        + A   +   Q+   P +      +QN+V + ++   + L+ + 
Sbjct: 5   HHHHHSSGLVPRGSHMMDAPDISYEHQETSVPNRSGIIPTLQNVVATVNLSCKLDLKNIA 64

Query: 115 GFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172
              A  + Y P+ F  +I R+++P  T LIF SGK+VITGAK+ +    A      ++
Sbjct: 65  -LRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGAKSEKSSRMAAQRYAKII 121

>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 =  219 bits (559), Expect = 3e-73
 Identities = 124/173 (71%), Positives = 147/173 (84%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
           P +QNIVAT+ L C+LDLK +ALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V T
Sbjct: 65  PTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVT 124

Query: 63  GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122
           GAKSE  +KLA+RKYARI+QKIGF  +F DFKIQNIVGSCDV+FPI+LE L   H  FS+
Sbjct: 125 GAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSS 184

Query: 123 YEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK RE+IY AF  IYPVL+ +
Sbjct: 185 YEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEF 237

>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 = 94.4 bits (234), Expect = 2e-24
 Identities = 36/141 (25%), Positives = 60/141 (42%), Gaps = 8/141 (5%)

Query: 36  RFSAVTMRIKEPKTTAL---IFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKD 92
            F      + +P T  +       G    T  +SE   K AA +  +             
Sbjct: 9   EFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSATSGI----V 64

Query: 93  FKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVI 152
             +QNIV +  +   + L+ +   HA  + Y P+ F  +I R+++P  T LIF SGK+V+
Sbjct: 65  PTLQNIVATVTLGCRLDLKTVA-LHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVV 123

Query: 153 TGAKAREQIYAAFNNIYPVLN 173
           TGAK+ +    A      ++ 
Sbjct: 124 TGAKSEDDSKLASRKYARIIQ 144

>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 =  214 bits (545), Expect = 7e-72
 Identities = 65/177 (36%), Positives = 101/177 (57%), Gaps = 2/177 (1%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           +   I+NIVA+++L  +LDL+K+     N++YNP  F  +   + +PK   LIFSSGK+V
Sbjct: 7   VKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLV 66

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAM 119
            TGAKS    + A  K A+ ++ IG    +     +QN+V S D+     L+ +      
Sbjct: 67  VTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLP- 125

Query: 120 FSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYV 176
              YEPE FPG+IYR+K+P   +L+F SGK+V +GAK+    + A   +   L+ Y+
Sbjct: 126 NCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKYL 182

>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 =  213 bits (543), Expect = 1e-71
 Identities = 124/175 (70%), Positives = 148/175 (84%)

Query: 1   MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
           + P +QNIVAT+ L C+LDLK +ALHARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 3   IVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 62

Query: 61  CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMF 120
            TGAKSE  +KLA+RKYARI+QKIGF  +F DFKIQNIVGSCDV+FPI+LE L   H  F
Sbjct: 63  VTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTF 122

Query: 121 STYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           S+YEPELFPGLIYRM KP + +LIF+SGK+V+TGAK RE+IY AF  IYPVL+ +
Sbjct: 123 SSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEF 177

>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 =  212 bits (542), Expect = 3e-71
 Identities = 70/174 (40%), Positives = 103/174 (59%), Gaps = 2/174 (1%)

Query: 3   PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT 62
             I+NIVAT+ L+  LDL  +     N EY+P +F  +  R++ PK T+LIF SGK+V T
Sbjct: 13  VNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVT 72

Query: 63  GAKSESQAKLAARKYARIVQKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFS 121
           GAKS  +   A ++  + ++K G  +      +IQNIV S ++   + L++        +
Sbjct: 73  GAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLE-NN 131

Query: 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
            YEPE FPGLIYRM +P V +LIF SGK+VITGAK  ++++ A   I+  L   
Sbjct: 132 MYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVEL 185

>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 = 90.4 bits (224), Expect = 3e-23
 Identities = 33/92 (35%), Positives = 51/92 (55%)

Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           IQNIVA+ NL   ++L K A    N  Y P +F  +  R+ EP+   LIFSSGK+V TGA
Sbjct: 106 IQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGA 165

Query: 65  KSESQAKLAARKYARIVQKIGFPVQFKDFKIQ 96
           K E +   A +K    + ++      ++ +++
Sbjct: 166 KREDEVHKAVKKIFDKLVELDCVKPVEEEELE 197

>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 = 75.8 bits (186), Expect = 1e-17
 Identities = 29/81 (35%), Positives = 47/81 (58%), Gaps = 1/81 (1%)

Query: 92  DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
              I+NIV +  ++  + L  +         Y+P+ FPGLI+R++ P +T LIF SGK+V
Sbjct: 12  VVNIENIVATVTLDQTLDLYAME-RSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMV 70

Query: 152 ITGAKAREQIYAAFNNIYPVL 172
           +TGAK+ +++  A   I   L
Sbjct: 71  VTGAKSTDELIKAVKRIIKTL 91

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

 Score =  208 bits (530), Expect = 1e-69
 Identities = 65/172 (37%), Positives = 99/172 (57%), Gaps = 2/172 (1%)

Query: 5   IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
           I N+V +  +   +DL+++A+   NAEY P +F  +  R+  PK   LIF SGK+ CTGA
Sbjct: 15  IVNVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGA 74

Query: 65  KSESQAKLAARKYARIVQKIGFP-VQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTY 123
           KS+ +A++A +K  + ++  G   ++  + KIQN+V + D+     L+ +       + Y
Sbjct: 75  KSKEEAEIAIKKIIKELKDAGIDVIENPEIKIQNMVATADLGIEPNLDDIALMVE-GTEY 133

Query: 124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY 175
           EPE FPGL+YR+  P V +LIF SGKVVITG K+ E    A   I   +   
Sbjct: 134 EPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKILDTIKEV 185

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

 Score = 75.8 bits (186), Expect = 1e-17
 Identities = 34/81 (41%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 92  DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
           + KI N+V S  +   I LE +       + YEPE FPGL+ R+  P V +LIF SGKV 
Sbjct: 12  EIKIVNVVVSTKIGDNIDLEEVA-MILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVN 70

Query: 152 ITGAKAREQIYAAFNNIYPVL 172
            TGAK++E+   A   I   L
Sbjct: 71  CTGAKSKEEAEIAIKKIIKEL 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	180
1ytb_A	180	Protein (tata binding protein (TBP)); protein-DNA	100.0
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	100.0
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	100.0
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	100.0
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	100.0
1mp9_A	198	Tata-binding protein; transcription regulation, DN	100.0
1rm1_A	240	Tata-box binding protein; yeast TFIIA, TBP protein	100.0
2z8u_A	188	Tata-box-binding protein; transcription, DNA-bindi	99.96
1mp9_A	198	Tata-binding protein; transcription regulation, DN	99.96
1ais_A	182	TBP, protein (tata-binding protein); hyperthermoph	99.96
1ytb_A	180	Protein (tata binding protein (TBP)); protein-DNA	99.95
3eik_A	218	Tata-box-binding protein; DNA-binding, initiation	99.94
3vn5_A	257	RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {A	94.15
2d0b_A	310	RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd	93.99
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	93.5
2d0b_A	310	RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd	92.84
3vn5_A	257	RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {A	92.75
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	82.12

>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=1.5e-71  Score=445.39  Aligned_cols=177  Identities=70%  Similarity=1.148  Sum_probs=174.3

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      |.|+|+|||||++++++|||++||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|+++++++
T Consensus         3 ~~~~I~NiVas~~l~~~ldL~~ia~~~~n~eYePe~fpgli~R~~~Pk~~~lIF~SGKiv~TGaks~e~~~~a~~~i~~~   82 (180)
T 1ytb_A            3 IVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARI   82 (180)
T ss_dssp             CCCEEEEEEEEEECCSCCCHHHHHHHSSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEEEEEcCCccCHHHHHhhCCCCEECccccCCEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           81 VQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        81 L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      |+++|+++++.+|+|||||||+|++|+|||++||..|.++++||||+||||+||+.+|+++++||+||||+|||||+++|
T Consensus        83 L~~lg~~~~~~~~~i~NIvas~dl~~~I~Le~la~~~~~~~~YEPE~fPGliyR~~~pkv~~lIF~SGkivitGak~~~~  162 (180)
T 1ytb_A           83 IQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREE  162 (180)
T ss_dssp             HHHHTCCCCCEEEEEEEEEEEEECSSCBCHHHHHHHTTTTEECCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHH
T ss_pred             HHHcCCCcccccceEEEEEEEEECCCccCHHHHHHhcccceEECCccCCcEEEEeCCCcEEEEEecCCeEEEEecCCHHH
Confidence            99999999999999999999999999999999998888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccc
Q 047239          161 IYAAFNNIYPVLNVYVT  177 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~  177 (180)
                      +++|+++|+|+|.+||+
T Consensus       163 ~~~a~~~i~p~L~~~~~  179 (180)
T 1ytb_A          163 IYQAFEAIYPVLSEFRK  179 (180)
T ss_dssp             HHHHHHHHHHHHHHTBC
T ss_pred             HHHHHHHHHHHHHHHhc
Confidence            99999999999999997

>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=3.1e-70  Score=447.73  Aligned_cols=178  Identities=65%  Similarity=1.070  Sum_probs=174.5

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      +.|+|+||||+++++|+|||++||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|+++++++
T Consensus        41 i~~~I~NIVas~~l~~~ldL~~ia~~~~n~eYePe~Fpglv~Rl~~Pk~t~LIF~SGKiV~TGAkS~e~a~~A~~ki~~~  120 (218)
T 3eik_A           41 IIPTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGAKSEKSSRMAAQRYAKI  120 (218)
T ss_dssp             CSCEEEEEEEEEECSSCCCHHHHHHHCTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEEEEECCCccCHHHHHhhCCCcEEcCccCceEEEEecCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           81 VQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        81 L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      |+++|+++++.+|+|||||||||++|+|||++|+..++++++||||+||||+||+.+|++|++||+||||+|||||+++|
T Consensus       121 L~~lG~~v~~~~fkIqNIvas~dl~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~pkvt~lIF~SGKiviTGaks~~d  200 (218)
T 3eik_A          121 IHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSNYCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDD  200 (218)
T ss_dssp             HHHTTCCCCCEEEEEEEEEEEEECSSCBCHHHHHHHSTTTEECCTTTSSSEEEEETTTTEEEEECTTSEEEEEEESSHHH
T ss_pred             HHHcCCCcccccceEEEEEEEEECCCcCcHHHHHHhccCCcEECCccCceEEEEcCCCCEEEEEeCCCeEEEEecCCHHH
Confidence            99999999999999999999999999999999998888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcccc
Q 047239          161 IYAAFNNIYPVLNVYVTY  178 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~~  178 (180)
                      +++|+++|+|+|.+|||.
T Consensus       201 ~~~A~~~I~p~L~~frk~  218 (218)
T 3eik_A          201 IYQAFNNIYPVLIQHRKA  218 (218)
T ss_dssp             HHHHHHHHHHHHHHTBC-
T ss_pred             HHHHHHHHHHHHHHhhcC
Confidence            999999999999999984

>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=9.6e-69  Score=445.11  Aligned_cols=178  Identities=70%  Similarity=1.141  Sum_probs=174.4

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      +.|+|+||||+++++|+|||++||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|+++++++
T Consensus        63 ~~~~I~NIVas~~l~~~ldL~~ia~~~~n~eYePe~Fpgli~Rl~~Pk~t~lIF~SGKiV~TGaks~e~a~~A~~~i~~~  142 (240)
T 1rm1_A           63 IVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARI  142 (240)
T ss_dssp             CCCEEEEEEEEEECCSCCCHHHHHHHBTTEEECTTTCSEEEEEEETTEEEEEEETTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CceEEEEEEEEEEcCCccCHHHHHhhCCCcEEcCcccceEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           81 VQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        81 L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      |+++|+++++.+|+|||||||+|++|+|||++|+..|.++++||||+||||+||+.+|+++++||+||||+|||+|+++|
T Consensus       143 L~~lg~~~~~~~f~IqNIVas~dl~f~I~Le~la~~~~~~~~YEPE~fPGLiyR~~~pkvvllIF~SGKIviTGaK~~~~  222 (240)
T 1rm1_A          143 IQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREE  222 (240)
T ss_dssp             HHHHTCCCCCEEEEEEEEEEEEECSSCBCHHHHHHHTTTTEEEETTTEEEEEEEETTTTEEEEECTTSEEEEEEESSHHH
T ss_pred             HHHcCCCcccCcceEEEEEEEEeCCCccCHHHHHHhchhccEECCccCCceEEEeCCCcEEEEEecCCEEEEEecCCHHH
Confidence            99999999999999999999999999999999999888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcccc
Q 047239          161 IYAAFNNIYPVLNVYVTY  178 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~~  178 (180)
                      +++|+++|+|+|.+||+.
T Consensus       223 ~~~Ai~~i~p~L~~~~~~  240 (240)
T 1rm1_A          223 IYQAFEAIYPVLSEFRKM  240 (240)
T ss_dssp             HHHHHHHHHHHHHHTBCC
T ss_pred             HHHHHHHHHHHHHHhccC
Confidence            999999999999999973

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

Probab=100.00  E-value=2.2e-67  Score=423.86  Aligned_cols=175  Identities=37%  Similarity=0.627  Sum_probs=163.4

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||+++++|+|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus        12 ~~~i~NvVas~~l~~~ldL~~ia~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~TGAkS~e~a~~a~~~~~~~L   91 (188)
T 2z8u_A           12 EIKIVNVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKSKEEAEIAIKKIIKEL   91 (188)
T ss_dssp             CCEEEEEEEEEECCSSCCHHHHHHHSSCCC-------CEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEEEEeCCeeCHHHHHhhCCCCEECCCCcccEEEEcCCCcEEEEEeCCCeEEEecCCCHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCC-CcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           82 QKIGFP-VQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        82 ~~~g~~-~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      +++|++ .++.+|+|+|||||++++++|||++|+.. .++++||||+||||+||+.+|++|++||+||||+||||||+++
T Consensus        92 ~~lg~~~~~~~~~~I~NIVas~~l~~~i~L~~la~~-~~~~eYePe~fPgliyR~~~Pk~t~lIF~SGKiviTGaks~~~  170 (188)
T 2z8u_A           92 KDAGIDVIENPEIKIQNMVATADLGIEPNLDDIALM-VEGTEYEPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEED  170 (188)
T ss_dssp             HHTTCCCCSSCCCEEEEEEEEEECSSCCCHHHHHHH-STTEEECTTTSSSEEEEEETTEEEEEECTTSEEEEESCSCHHH
T ss_pred             HhcCCCccccCceEEEEEEEEEecCCccCHHHHHhh-CcCcEECCccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHH
Confidence            999998 58889999999999999999999999986 7899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccc
Q 047239          161 IYAAFNNIYPVLNVYVT  177 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~  177 (180)
                      ++.|+++|+|+|.+|++
T Consensus       171 ~~~A~~~i~~~L~~~~~  187 (188)
T 2z8u_A          171 AKRALKKILDTIKEVQE  187 (188)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            99999999999999875

>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=7.7e-67  Score=419.00  Aligned_cols=173  Identities=38%  Similarity=0.592  Sum_probs=168.9

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||+++++|+|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus         8 ~~~I~NvVas~~l~~~ldL~~ia~~~~n~eY~P~~fpgli~Rl~~P~~t~lIF~SGKiv~TGakS~~~~~~a~~~i~~~L   87 (182)
T 1ais_A            8 KLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKL   87 (182)
T ss_dssp             EEEEEEEEEEEECCSCCCHHHHTTTSTTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEEcCCeeCHHHHHhhCCCcEECCCccccEEEEcCCCcEEEEEeCCCeEEEecCCCHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCC-CcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           82 QKIGFP-VQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        82 ~~~g~~-~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      +++|++ .++.+|+|+|||||++++++|||++|+.. .++++||||+||||+||+.+|++|++||+||||+||||||+++
T Consensus        88 ~~lG~~~~~~~~~~I~NIVas~~l~~~i~L~~la~~-~~~~~YePe~fpgli~R~~~pk~~~lIF~SGKiviTGaks~~~  166 (182)
T 1ais_A           88 KSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALT-LPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEAD  166 (182)
T ss_dssp             HHTTCCCSSSCEEEEEEEEEEEECSSCCCHHHHHHH-STTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHH
T ss_pred             HHcCCCcccccceEEEEEEEEEEcCCccCHHHHHhh-CCCCEECCccCceEEEEeCCCcEEEEEecCCEEEEEecCCHHH
Confidence            999998 58889999999999999999999999986 7899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhc
Q 047239          161 IYAAFNNIYPVLNVY  175 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~  175 (180)
                      ++.|+++|+|+|.+|
T Consensus       167 ~~~a~~~i~~~L~~~  181 (182)
T 1ais_A          167 AWEAVRKLLRELDKY  181 (182)
T ss_dssp             HHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999999886

>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=1.9e-66  Score=421.35  Aligned_cols=176  Identities=40%  Similarity=0.627  Sum_probs=171.2

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+|||||++++|+|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus        12 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~TGakS~e~a~~a~~~i~~~L   91 (198)
T 1mp9_A           12 VVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTL   91 (198)
T ss_dssp             EEEEEEEEEEEECCSCCCHHHHHHHSTTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccccceEEEcCCCceEEEEeCCCeEEEeccCCHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCC-CcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239           82 QKIGFP-VQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ  160 (180)
Q Consensus        82 ~~~g~~-~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~  160 (180)
                      +++|++ .++.+|+|+|||||++++++|||++|+.. .++++||||+||||+||+.+|++|++||+||||+||||||+++
T Consensus        92 ~~lG~~~~~~~~~~I~NIVas~~l~~~i~L~~la~~-~~~~~YePe~fPgliyR~~~Pk~t~lIF~SGKiviTGaks~~~  170 (198)
T 1mp9_A           92 KKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFL-LENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDE  170 (198)
T ss_dssp             HHTTCCCSSCCEEEEEEEEEEEECSSEECHHHHHHH-SSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHH
T ss_pred             HHcCCcccCcCceEEEEEEEEeeCCCccCHHHHHhh-cCCcEECCccCCeEEEEeCCCcEEEEEeCCCEEEEEecCCHHH
Confidence            999998 58889999999999999999999999986 7899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcccc
Q 047239          161 IYAAFNNIYPVLNVYVTY  178 (180)
Q Consensus       161 ~~~a~~~i~~~L~~~~~~  178 (180)
                      ++.|+++|+|+|.+++..
T Consensus       171 ~~~A~~~i~~~L~~~~~~  188 (198)
T 1mp9_A          171 VHKAVKKIFDKLVELDCV  188 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHHHhCCC
Confidence            999999999999998753

>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=3.3e-34  Score=237.82  Aligned_cols=123  Identities=27%  Similarity=0.278  Sum_probs=83.2

Q ss_pred             EEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCC
Q 047239           49 TTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELF  128 (180)
Q Consensus        49 ~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~f  128 (180)
                      +--+=|+|||+++||++|.++++.++    +.++++|.+....+++|+||||+++++++|||++|+.. .++++||||+|
T Consensus        25 ~~~~~f~sGk~~~s~~~s~~~~~~~~----~~~~~~~~~~~~~~~~I~NIVas~~l~~~ldL~~ia~~-~~n~eYePe~F   99 (240)
T 1rm1_A           25 VWENQNRDGTKPATTFQSEEDIKRAA----PESEKDTSATSGIVPTLQNIVATVTLGCRLDLKTVALH-ARNAEYNPKRF   99 (240)
T ss_dssp             ----------------------------------------CCCCCEEEEEEEEEECCSCCCHHHHHHH-BTTEEECTTTC
T ss_pred             cccccCCCCcceecccccHHHHHHHH----HHHHhhccCcCCCceEEEEEEEEEEcCCccCHHHHHhh-CCCcEEcCccc
Confidence            33467999999999999988876665    55566666666668999999999999999999999975 88999999999


Q ss_pred             ceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHHHhhcc
Q 047239          129 PGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYV  176 (180)
Q Consensus       129 pgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~~~  176 (180)
                      |||+||+.+|+++++||+||||+||||||+++++.|+++++++|.++.
T Consensus       100 pgli~Rl~~Pk~t~lIF~SGKiV~TGaks~e~a~~A~~~i~~~L~~lg  147 (240)
T 1rm1_A          100 AAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIG  147 (240)
T ss_dssp             SEEEEEEETTEEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHHHHHT
T ss_pred             ceEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence            999999999999999999999999999999999999999999998864

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

Probab=99.96  E-value=5.5e-30  Score=205.98  Aligned_cols=85  Identities=40%  Similarity=0.598  Sum_probs=82.3

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+|||||++++++|||+.||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|++++.++|
T Consensus       103 ~~~I~NIVas~~l~~~i~L~~la~~~~~~eYePe~fPgliyR~~~Pk~t~lIF~SGKiviTGaks~~~~~~A~~~i~~~L  182 (188)
T 2z8u_A          103 EIKIQNMVATADLGIEPNLDDIALMVEGTEYEPEQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKILDTI  182 (188)
T ss_dssp             CCEEEEEEEEEECSSCCCHHHHHHHSTTEEECTTTSSSEEEEEETTEEEEEECTTSEEEEESCSCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEecCCccCHHHHHhhCcCcEECCccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCC
Q 047239           82 QKIGF   86 (180)
Q Consensus        82 ~~~g~   86 (180)
                      +++|+
T Consensus       183 ~~~~~  187 (188)
T 2z8u_A          183 KEVQE  187 (188)
T ss_dssp             HHHC-
T ss_pred             HHhcc
Confidence            99874

>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=99.96  E-value=1.5e-29  Score=204.89  Aligned_cols=86  Identities=38%  Similarity=0.550  Sum_probs=83.6

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+|||||++++++|||+.||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|++++.++|
T Consensus       103 ~~~I~NIVas~~l~~~i~L~~la~~~~~~~YePe~fPgliyR~~~Pk~t~lIF~SGKiviTGaks~~~~~~A~~~i~~~L  182 (198)
T 1mp9_A          103 KIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKL  182 (198)
T ss_dssp             EEEEEEEEEEEECSSEECHHHHHHHSSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEeeCCCccCHHHHHhhcCCcEECCccCCeEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCC
Q 047239           82 QKIGFP   87 (180)
Q Consensus        82 ~~~g~~   87 (180)
                      +++|+.
T Consensus       183 ~~~~~~  188 (198)
T 1mp9_A          183 VELDCV  188 (198)
T ss_dssp             HHTTCE
T ss_pred             HHhCCC
Confidence            999874

>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=99.96  E-value=2.1e-29  Score=201.77  Aligned_cols=83  Identities=45%  Similarity=0.664  Sum_probs=80.3

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+|||||++++++|||+.||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|++++.++|
T Consensus        99 ~~~I~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpgli~R~~~pk~~~lIF~SGKiviTGaks~~~~~~a~~~i~~~L  178 (182)
T 1ais_A           99 QIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLREL  178 (182)
T ss_dssp             EEEEEEEEEEEECSSCCCHHHHHHHSTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEEcCCccCHHHHHhhCCCCEECCccCceEEEEeCCCcEEEEEecCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHc
Q 047239           82 QKI   84 (180)
Q Consensus        82 ~~~   84 (180)
                      +++
T Consensus       179 ~~~  181 (182)
T 1ais_A          179 DKY  181 (182)
T ss_dssp             TTC
T ss_pred             HHh
Confidence            764

>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=99.95  E-value=3e-28  Score=194.63  Aligned_cols=84  Identities=30%  Similarity=0.444  Sum_probs=80.5

Q ss_pred             ceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHH
Q 047239           92 DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPV  171 (180)
Q Consensus        92 ~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~  171 (180)
                      .++|+|||||++++++|||++||.. .++++||||+||||+||+.+|+++++||+||||+||||||+++++.|+++++++
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 VPTLQNIVATVTLGCRLDLKTVALH-ARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARI   82 (180)
T ss_dssp             CCEEEEEEEEEECCSCCCHHHHHHH-SSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             ceEEEEEEEEEEcCCccCHHHHHhh-CCCCEECccccCCEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            5789999999999999999999974 899999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhcc
Q 047239          172 LNVYV  176 (180)
Q Consensus       172 L~~~~  176 (180)
                      |.++-
T Consensus        83 L~~lg   87 (180)
T 1ytb_A           83 IQKIG   87 (180)
T ss_dssp             HHHHT
T ss_pred             HHHcC
Confidence            98764

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

Probab=99.94  E-value=1.7e-26  Score=188.82  Aligned_cols=83  Identities=31%  Similarity=0.444  Sum_probs=79.4

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhC-CCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHA-RNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~-~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      .++|+||||+++++++|||+.||... ++++||||+||||+||+.+|+++++||+||||+|||+||++|++.|++++.++
T Consensus       132 ~fkIqNIvas~dl~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~pkvt~lIF~SGKiviTGaks~~d~~~A~~~I~p~  211 (218)
T 3eik_A          132 DFKIQNIVSSCDIKFSIRLEGLAYAHSNYCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPV  211 (218)
T ss_dssp             EEEEEEEEEEEECSSCBCHHHHHHHSTTTEECCTTTSSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             cceEEEEEEEEECCCcCcHHHHHHhccCCcEECCccCceEEEEcCCCCEEEEEeCCCeEEEEecCCHHHHHHHHHHHHHH
Confidence            37899999999999999999999764 79999999999999999999999999999999999999999999999999999


Q ss_pred             HHHc
Q 047239           81 VQKI   84 (180)
Q Consensus        81 L~~~   84 (180)
                      |.++
T Consensus       212 L~~f  215 (218)
T 3eik_A          212 LIQH  215 (218)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            9875

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

Probab=94.15  E-value=0.016  Score=48.05  Aligned_cols=38  Identities=13%  Similarity=0.194  Sum_probs=31.5

Q ss_pred             CCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHH
Q 047239           34 PSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAK   71 (180)
Q Consensus        34 Pe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~   71 (180)
                      +..=|+..++.+.+.+++.+|.|||++.+|...++.+.
T Consensus        25 ~~~~~~~~f~~k~~~~~it~Y~SGkv~fqG~~a~~~a~   62 (257)
T 3vn5_A           25 KINAPYTLWALEGNGVKVYYYKTGSLLIQGKNSEKVLK   62 (257)
T ss_dssp             ECCCTTCSEEEEETTEEEEECTTSEEEEESTTHHHHHH
T ss_pred             ccCCCceEEEEecCCeEEEEEeccEEEEeCCCHHHHHH
Confidence            34457899999999999999999999999996655543

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

Probab=93.99  E-value=0.077  Score=44.97  Aligned_cols=36  Identities=22%  Similarity=0.398  Sum_probs=31.0

Q ss_pred             CccceEEEEecCCcEEEEEecCCcEEEEccCCHHHH
Q 047239           35 SRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQA   70 (180)
Q Consensus        35 e~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~   70 (180)
                      ..-|+..|+.+.+.+++.+|.|||++.+|..+++.+
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            345899999999999999999999999998665444

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=93.50  E-value=1.2  Score=33.28  Aligned_cols=30  Identities=23%  Similarity=0.056  Sum_probs=24.6

Q ss_pred             eEEEEcccCHHHHHHHHHHHHHHHhhccccCC
Q 047239          149 KVVITGAKAREQIYAAFNNIYPVLNVYVTYDQ  180 (180)
Q Consensus       149 kivitGaks~~~~~~a~~~i~~~L~~~~~~~~  180 (180)
                      .|.|+|  +.+.+..|...|..++.+.+..+|
T Consensus       133 ~v~I~G--~~~~v~~A~~~I~~~i~~~~~~~~  162 (163)
T 3krm_A          133 IVKIIG--HFYASQMAQRKIRDILAQVKQQHQ  162 (163)
T ss_dssp             EEEEEE--CHHHHHHHHHHHHHHHHHHTC---
T ss_pred             EEEEEe--CHHHHHHHHHHHHHHHHHHHHhhc
Confidence            588999  578999999999999999998776

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

Probab=92.84  E-value=0.1  Score=44.24  Aligned_cols=36  Identities=31%  Similarity=0.621  Sum_probs=31.0

Q ss_pred             cCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239          126 ELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI  161 (180)
Q Consensus       126 e~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~  161 (180)
                      ..-|+..|+...+.+++.+|.||||++.|...+..+
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            445899999999999999999999999998765433

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

Probab=92.75  E-value=0.059  Score=44.63  Aligned_cols=39  Identities=13%  Similarity=0.300  Sum_probs=32.6

Q ss_pred             CCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHH
Q 047239          124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIY  162 (180)
Q Consensus       124 ePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~  162 (180)
                      ++..=|+..|+...+.+|+.+|.||||++.|...+..+.
T Consensus        24 ~~~~~~~~~f~~k~~~~~it~Y~SGkv~fqG~~a~~~a~   62 (257)
T 3vn5_A           24 RKINAPYTLWALEGNGVKVYYYKTGSLLIQGKNSEKVLK   62 (257)
T ss_dssp             EECCCTTCSEEEEETTEEEEECTTSEEEEESTTHHHHHH
T ss_pred             cccCCCceEEEEecCCeEEEEEeccEEEEeCCCHHHHHH
Confidence            455568999999999999999999999999997654443

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=82.12  E-value=12  Score=27.52  Aligned_cols=26  Identities=19%  Similarity=0.280  Sum_probs=22.7

Q ss_pred             CceEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239          147 SGKVVITGAKAREQIYAAFNNIYPVLNV  174 (180)
Q Consensus       147 sGkivitGaks~~~~~~a~~~i~~~L~~  174 (180)
                      .+.|.|+|  +++.+..|.+.|..++.+
T Consensus       134 ~~~v~I~G--~~~~v~~A~~~I~~~i~e  159 (160)
T 2jzx_A          134 ERAITIAG--IPQSIIECVKQICVVMLE  159 (160)
T ss_dssp             EEEEEEEE--CHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEEEc--CHHHHHHHHHHHHHHHhc
Confidence            57899999  589999999999988875

---

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	180
d1qnaa1	99	d.129.1.1 (A:17-115) TATA-box binding protein (TBP	8e-45
d1qnaa1	99	d.129.1.1 (A:17-115) TATA-box binding protein (TBP	2e-27
d1aisa1	92	d.129.1.1 (A:1-92) TATA-box binding protein (TBP),	4e-37
d1aisa1	92	d.129.1.1 (A:1-92) TATA-box binding protein (TBP),	1e-31
d1mp9a1	92	d.129.1.1 (A:5-96) TATA-box binding protein (TBP),	2e-36
d1mp9a1	92	d.129.1.1 (A:5-96) TATA-box binding protein (TBP),	1e-28
d1mp9a2	101	d.129.1.1 (A:97-197) TATA-box binding protein (TBP	9e-35
d1mp9a2	101	d.129.1.1 (A:97-197) TATA-box binding protein (TBP	2e-31
d1aisa2	89	d.129.1.1 (A:93-181) TATA-box binding protein (TBP	2e-34
d1aisa2	89	d.129.1.1 (A:93-181) TATA-box binding protein (TBP	2e-31
d1qnaa2	83	d.129.1.1 (A:116-198) TATA-box binding protein (TB	4e-31
d1qnaa2	83	d.129.1.1 (A:116-198) TATA-box binding protein (TB	4e-28

>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 =  141 bits (357), Expect = 8e-45
 Identities = 73/95 (76%), Positives = 86/95 (90%)

Query: 1  MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
          + P +QNIV+T+NL+CKLDLK IAL ARNAEYNP RF+AV MRI+EPKTTALIF+SGK+V
Sbjct: 5  IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMV 64

Query: 61 CTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKI 95
          CTGAKSE  +K+AARKYARIVQK+GFP +FKDFKI
Sbjct: 65 CTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKI 99

>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 = 97.1 bits (242), Expect = 2e-27
 Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 94  KIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVIT 153
            +QNIV + +++  + L+ +    A  + Y P+ F  +I R+++P  T LIF SGK+V T
Sbjct: 8   TLQNIVSTVNLDCKLDLKAIA-LQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCT 66

Query: 154 GAKAREQIYAAFNNIYPVL 172
           GAK+ +    A      ++
Sbjct: 67  GAKSEDFSKMAARKYARIV 85

>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 =  121 bits (305), Expect = 4e-37
 Identities = 35/85 (41%), Positives = 53/85 (62%)

Query: 1  MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIV 60
          +   I+NIVA+++L  +LDL+K+     N++YNP  F  +   + +PK   LIFSSGK+V
Sbjct: 7  VKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLV 66

Query: 61 CTGAKSESQAKLAARKYARIVQKIG 85
           TGAKS    + A  K A+ ++ IG
Sbjct: 67 VTGAKSVQDIERAVAKLAQKLKSIG 91

>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 =  107 bits (270), Expect = 1e-31
 Identities = 32/82 (39%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 92  DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
             +I+NIV S D+   + LE++       S Y PE FPG+I  +  P V +LIF SGK+V
Sbjct: 8   KLRIENIVASVDLFAQLDLEKVL-DLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLV 66

Query: 152 ITGAKAREQIYAAFNNIYPVLN 173
           +TGAK+ + I  A   +   L 
Sbjct: 67  VTGAKSVQDIERAVAKLAQKLK 88

>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 =  120 bits (302), Expect = 2e-36
 Identities = 34/81 (41%), Positives = 51/81 (62%)

Query: 5  IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
          I+NIVAT+ L+  LDL  +     N EY+P +F  +  R++ PK T+LIF SGK+V TGA
Sbjct: 11 IENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGA 70

Query: 65 KSESQAKLAARKYARIVQKIG 85
          KS  +   A ++  + ++K G
Sbjct: 71 KSTDELIKAVKRIIKTLKKYG 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 =  100 bits (250), Expect = 1e-28
 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 1/82 (1%)

Query: 92  DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
              I+NIV +  ++  + L  +         Y+P+ FPGLI+R++ P +T LIF SGK+V
Sbjct: 8   VVNIENIVATVTLDQTLDLYAME-RSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMV 66

Query: 152 ITGAKAREQIYAAFNNIYPVLN 173
           +TGAK+ +++  A   I   L 
Sbjct: 67  VTGAKSTDELIKAVKRIIKTLK 88

>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 =  116 bits (291), Expect = 9e-35
 Identities = 33/81 (40%), Positives = 46/81 (56%)

Query: 5  IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
          IQNIVA+ NL   ++L K A    N  Y P +F  +  R+ EP+   LIFSSGK+V TGA
Sbjct: 10 IQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGA 69

Query: 65 KSESQAKLAARKYARIVQKIG 85
          K E +   A +K    + ++ 
Sbjct: 70 KREDEVHKAVKKIFDKLVELD 90

>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 =  107 bits (268), Expect = 2e-31
 Identities = 40/92 (43%), Positives = 55/92 (59%), Gaps = 5/92 (5%)

Query: 82  QKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVT 141
           Q  G P      +IQNIV S ++   + L++   F    + YEPE FPGLIYRM +P V 
Sbjct: 1   QLTGKP----KIQIQNIVASANLHVIVNLDKAA-FLLENNMYEPEQFPGLIYRMDEPRVV 55

Query: 142 MLIFLSGKVVITGAKAREQIYAAFNNIYPVLN 173
           +LIF SGK+VITGAK  ++++ A   I+  L 
Sbjct: 56  LLIFSSGKMVITGAKREDEVHKAVKKIFDKLV 87

>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 (287), Expect = 2e-34
 Identities = 37/79 (46%), Positives = 52/79 (65%)

Query: 5  IQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
          +QN+V + ++  + +L  +AL   N EY P +F  V  R+KEPK+  L+FSSGKIVC+GA
Sbjct: 10 VQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGA 69

Query: 65 KSESQAKLAARKYARIVQK 83
          KSE+ A  A RK  R + K
Sbjct: 70 KSEADAWEAVRKLLRELDK 88

>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 =  106 bits (267), Expect = 2e-31
 Identities = 30/84 (35%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 92  DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV 151
              +QN+V S D+     L+ +         YEPE FPG+IYR+K+P   +L+F SGK+V
Sbjct: 7   QIDVQNMVFSGDIGREFNLDVVA-LTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIV 65

Query: 152 ITGAKAREQIYAAFNNIYPVLNVY 175
            +GAK+    + A   +   L+ Y
Sbjct: 66  CSGAKSEADAWEAVRKLLRELDKY 89

>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 =  105 bits (265), Expect = 4e-31
 Identities = 56/80 (70%), Positives = 67/80 (83%)

Query: 96  QNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGA 155
           QNIVGSCDV+FPI+LE L   HA FS+YEPELFPGLIYRMK P + +LIF+SGK+VITGA
Sbjct: 1   QNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGA 60

Query: 156 KAREQIYAAFNNIYPVLNVY 175
           K R++ Y AF NIYPVL+ +
Sbjct: 61  KMRDETYKAFENIYPVLSEF 80

>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 = 98.3 bits (245), Expect = 4e-28
 Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 6  QNIVATINLECKLDLKKIAL-HARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGA 64
          QNIV + +++  + L+ +A  HA  + Y P  F  +  R+K PK   LIF SGKIV TGA
Sbjct: 1  QNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGA 60

Query: 65 KSESQAKLAARKYARIVQK 83
          K   +   A      ++ +
Sbjct: 61 KMRDETYKAFENIYPVLSE 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	180
d1qnaa1	99	TATA-box binding protein (TBP), C-terminal domain	100.0
d1qnaa2	83	TATA-box binding protein (TBP), C-terminal domain	100.0
d1mp9a1	92	TATA-box binding protein (TBP), C-terminal domain	100.0
d1aisa1	92	TATA-box binding protein (TBP), C-terminal domain	100.0
d1aisa2	89	TATA-box binding protein (TBP), C-terminal domain	100.0
d1aisa2	89	TATA-box binding protein (TBP), C-terminal domain	99.98
d1aisa1	92	TATA-box binding protein (TBP), C-terminal domain	99.97
d1mp9a2	101	TATA-box binding protein (TBP), C-terminal domain	99.97
d1mp9a2	101	TATA-box binding protein (TBP), C-terminal domain	99.97
d1mp9a1	92	TATA-box binding protein (TBP), C-terminal domain	99.97
d1qnaa1	99	TATA-box binding protein (TBP), C-terminal domain	99.97
d1qnaa2	83	TATA-box binding protein (TBP), C-terminal domain	99.97

>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=9.4e-38  Score=226.18  Aligned_cols=95  Identities=77%  Similarity=1.206  Sum_probs=93.3

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      ++|+|+||||+++++++|||++||.+++|++||||+||||+||+++|+++++||+||||+||||+|+++++.|++++.++
T Consensus         5 ~~p~i~NiVas~~l~~~idL~~la~~~~n~eYePe~fpgli~R~~~P~~t~lIF~SGKivitGaks~~~~~~a~~~i~~~   84 (99)
T d1qnaa1           5 IVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARI   84 (99)
T ss_dssp             CCCEEEEEEEEEECCSCCCHHHHHHHCSSEEECTTTCSEEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEEEcCCcccHHHHHhhCCCCEECcccCCEEEEEeCCCcEEEEEEcCCEEEEeccCCHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCcccceee
Q 047239           81 VQKIGFPVQFKDFKI   95 (180)
Q Consensus        81 L~~~g~~~~~~~~~i   95 (180)
                      |+++|+++++.+|+|
T Consensus        85 l~k~g~~v~~~~f~i   99 (99)
T d1qnaa1          85 VQKLGFPAKFKDFKI   99 (99)
T ss_dssp             HHHTTCCCCCEEEEE
T ss_pred             HHHcCCCCcccccCC
Confidence            999999999999986

>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=1e-34  Score=203.89  Aligned_cols=82  Identities=68%  Similarity=1.167  Sum_probs=80.3

Q ss_pred             eeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHHHhhc
Q 047239           96 QNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVY  175 (180)
Q Consensus        96 ~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~~  175 (180)
                      ||||||++++++|||++||..+..+++||||+||||+||+.+|+++++||+||||+||||||++++++|++.|+|+|.+|
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            79999999999999999998888899999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 047239          176 VT  177 (180)
Q Consensus       176 ~~  177 (180)
                      ||
T Consensus        81 ~k   82 (83)
T d1qnaa2          81 RK   82 (83)
T ss_dssp             BC
T ss_pred             cc
Confidence            97

>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=1.3e-33  Score=201.67  Aligned_cols=85  Identities=40%  Similarity=0.647  Sum_probs=83.0

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||+++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||||+++++.|++++.++|
T Consensus         8 ~~~i~NiVas~~l~~~idL~~la~~~~~~~YePe~fpgli~R~~~p~~t~lIF~SGkivitGaks~~~~~~a~~~~~~~L   87 (92)
T d1mp9a1           8 VVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTL   87 (92)
T ss_dssp             EEEEEEEEEEEECCSCCCHHHHHHHSTTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEEEEECCCcccHHHHHhhCCCCEECCccCceEEEEECCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCC
Q 047239           82 QKIGF   86 (180)
Q Consensus        82 ~~~g~   86 (180)
                      +++|.
T Consensus        88 ~~~G~   92 (92)
T d1mp9a1          88 KKYGM   92 (92)
T ss_dssp             HHTTC
T ss_pred             HHcCC
Confidence            99984

>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=1.4e-33  Score=201.62  Aligned_cols=86  Identities=41%  Similarity=0.623  Sum_probs=83.6

Q ss_pred             CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239            1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI   80 (180)
Q Consensus         1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~   80 (180)
                      +.++|+||||+++++++|||++||.+++|++||||+|||++||+++|+++++||+|||++||||||+++++.|++++.++
T Consensus         7 ~~~~I~NiVas~~l~~~idL~~la~~~~~~~YePe~fpgl~~R~~~p~~~~lIF~sGkivitGakS~~~~~~a~~~i~~~   86 (92)
T d1aisa1           7 VKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQK   86 (92)
T ss_dssp             CEEEEEEEEEEEECCSCCCHHHHTTTSTTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEEEEECCCCccHHHHHhhCCCCEECcccCCeEEEEeCCCcEEEEEECCCEEEEEccCCHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCC
Q 047239           81 VQKIGF   86 (180)
Q Consensus        81 L~~~g~   86 (180)
                      |+++|.
T Consensus        87 l~~lGv   92 (92)
T d1aisa1          87 LKSIGV   92 (92)
T ss_dssp             HHHTTC
T ss_pred             HHHcCC
Confidence            999984

>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=4.3e-33  Score=197.89  Aligned_cols=83  Identities=36%  Similarity=0.610  Sum_probs=80.3

Q ss_pred             ceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHH
Q 047239           92 DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPV  171 (180)
Q Consensus        92 ~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~  171 (180)
                      +++|+||||+++++++|||++|+.. .++++||||+||||+||+.+|+++++||+||||+||||||+++++.|++.++|+
T Consensus         7 ~i~I~NiVas~~l~~~idL~~la~~-~~~~~Y~Pe~fpgli~R~~~p~~t~lIF~SGKivitGaks~~~~~~a~~~i~~~   85 (89)
T d1aisa2           7 QIDVQNMVFSGDIGREFNLDVVALT-LPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRE   85 (89)
T ss_dssp             EEEEEEEEEEEECSSCCCHHHHHHH-STTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEEEEECCCcccHHHHHhh-ccCcEECcccCceEEEEEcCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHHH
Confidence            5899999999999999999999986 579999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhc
Q 047239          172 LNVY  175 (180)
Q Consensus       172 L~~~  175 (180)
                      |.+|
T Consensus        86 L~k~   89 (89)
T d1aisa2          86 LDKY   89 (89)
T ss_dssp             HTTC
T ss_pred             HhcC
Confidence            9987

>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=99.98  E-value=6e-33  Score=197.15  Aligned_cols=83  Identities=45%  Similarity=0.664  Sum_probs=80.3

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||+++++++|||++||..++|++||||+||||+||+++|+++++||+||||+||||||+++++.|++++.++|
T Consensus         7 ~i~I~NiVas~~l~~~idL~~la~~~~~~~Y~Pe~fpgli~R~~~p~~t~lIF~SGKivitGaks~~~~~~a~~~i~~~L   86 (89)
T d1aisa2           7 QIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLREL   86 (89)
T ss_dssp             EEEEEEEEEEEECSSCCCHHHHHHHSTTEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEEEEECCCcccHHHHHhhccCcEECcccCceEEEEEcCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHHHH
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHc
Q 047239           82 QKI   84 (180)
Q Consensus        82 ~~~   84 (180)
                      ++.
T Consensus        87 ~k~   89 (89)
T d1aisa2          87 DKY   89 (89)
T ss_dssp             TTC
T ss_pred             hcC
Confidence            863

>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=99.97  E-value=3e-32  Score=194.57  Aligned_cols=88  Identities=36%  Similarity=0.562  Sum_probs=83.0

Q ss_pred             CCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239           87 PVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFN  166 (180)
Q Consensus        87 ~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~  166 (180)
                      +++..+++|+||||+++++++|||++|+. +.++++||||+||||+||+.+|+++++||+||||+||||||+++++.|++
T Consensus         3 d~~~~~~~I~NiVas~~l~~~idL~~la~-~~~~~~YePe~fpgl~~R~~~p~~~~lIF~sGkivitGakS~~~~~~a~~   81 (92)
T d1aisa1           3 DMSKVKLRIENIVASVDLFAQLDLEKVLD-LCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVA   81 (92)
T ss_dssp             CCTTCEEEEEEEEEEEECCSCCCHHHHTT-TSTTCBCCTTTCSSEEEECSSSCCEEEECTTSEEEEEEESSHHHHHHHHH
T ss_pred             CcCcCcEEEEEEEEEEECCCCccHHHHHh-hCCCCEECcccCCeEEEEeCCCcEEEEEECCCEEEEEccCCHHHHHHHHH
Confidence            45566899999999999999999999986 47899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhc
Q 047239          167 NIYPVLNVY  175 (180)
Q Consensus       167 ~i~~~L~~~  175 (180)
                      +++++|.+.
T Consensus        82 ~i~~~l~~l   90 (92)
T d1aisa1          82 KLAQKLKSI   90 (92)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHc
Confidence            999999874

>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=99.97  E-value=4.8e-32  Score=196.61  Aligned_cols=85  Identities=39%  Similarity=0.563  Sum_probs=82.9

Q ss_pred             CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239            2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV   81 (180)
Q Consensus         2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L   81 (180)
                      .++|+||||+++++++|||++||..++|++||||+||||+||+++|+++++||+||||+||||+|+++++.|++++.++|
T Consensus         7 ~~~v~NiVas~~l~~~idL~~la~~~~~~~YePe~fpgli~R~~~pk~t~lIF~SGKivitGaks~~~~~~a~~~i~~~L   86 (101)
T d1mp9a2           7 KIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKL   86 (101)
T ss_dssp             EEEEEEEEEEEECSSEECHHHHHHHSSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEEEEEECCCcccHHHHHhhCCCCEECcccCCeEEEEecCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCC
Q 047239           82 QKIGF   86 (180)
Q Consensus        82 ~~~g~   86 (180)
                      ++++.
T Consensus        87 ~~~~~   91 (101)
T d1mp9a2          87 VELDC   91 (101)
T ss_dssp             HHTTC
T ss_pred             HHhCC
Confidence            99985

>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=99.97  E-value=3.6e-32  Score=197.25  Aligned_cols=86  Identities=42%  Similarity=0.665  Sum_probs=82.5

Q ss_pred             cceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHH
Q 047239           91 KDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYP  170 (180)
Q Consensus        91 ~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~  170 (180)
                      .+++|+||||+++++++|||++||.. .++++||||+||||+||+.+|+++++||+||||+|||++|+++++.|+++|+|
T Consensus         6 p~~~v~NiVas~~l~~~idL~~la~~-~~~~~YePe~fpgli~R~~~pk~t~lIF~SGKivitGaks~~~~~~a~~~i~~   84 (101)
T d1mp9a2           6 PKIQIQNIVASANLHVIVNLDKAAFL-LENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFD   84 (101)
T ss_dssp             CEEEEEEEEEEEECSSEECHHHHHHH-SSSEECCTTTCSSEEEEETTTTEEEEECTTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEEEEECCCcccHHHHHhh-CCCCEECcccCCeEEEEecCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHH
Confidence            37899999999999999999999986 57899999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccc
Q 047239          171 VLNVYVT  177 (180)
Q Consensus       171 ~L~~~~~  177 (180)
                      +|.+++.
T Consensus        85 ~L~~~~~   91 (101)
T d1mp9a2          85 KLVELDC   91 (101)
T ss_dssp             HHHHTTC
T ss_pred             HHHHhCC
Confidence            9999984

>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=99.97  E-value=5.6e-32  Score=193.18  Aligned_cols=83  Identities=36%  Similarity=0.655  Sum_probs=80.1

Q ss_pred             ceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHH
Q 047239           92 DFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPV  171 (180)
Q Consensus        92 ~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~  171 (180)
                      .++|+|||||++++++|||++|+.. .++++||||+||||+||+.+|+++++||+||||+||||||+++++.|+++++++
T Consensus         8 ~~~i~NiVas~~l~~~idL~~la~~-~~~~~YePe~fpgli~R~~~p~~t~lIF~SGkivitGaks~~~~~~a~~~~~~~   86 (92)
T d1mp9a1           8 VVNIENIVATVTLDQTLDLYAMERS-VPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKT   86 (92)
T ss_dssp             EEEEEEEEEEEECCSCCCHHHHHHH-STTCBCCTTTCSSEEEEETTTTEEEEECTTSEEEEECCSSHHHHHHHHHHHHHH
T ss_pred             eEEEEEEEEEEECCCcccHHHHHhh-CCCCEECCccCceEEEEECCCcEEEEEEcCCEEEEEccCCHHHHHHHHHHHHHH
Confidence            5889999999999999999999986 689999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhc
Q 047239          172 LNVY  175 (180)
Q Consensus       172 L~~~  175 (180)
                      |.++
T Consensus        87 L~~~   90 (92)
T d1mp9a1          87 LKKY   90 (92)
T ss_dssp             HHHT
T ss_pred             HHHc
Confidence            9876

>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=99.97  E-value=1.8e-31  Score=192.84  Aligned_cols=84  Identities=30%  Similarity=0.437  Sum_probs=80.5

Q ss_pred             cceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHH
Q 047239           91 KDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYP  170 (180)
Q Consensus        91 ~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~  170 (180)
                      -.++|+||||+++++++|||++||.. .++++||||+||||+||+.+|+++++||+||||+||||||+++++.|++++++
T Consensus         5 ~~p~i~NiVas~~l~~~idL~~la~~-~~n~eYePe~fpgli~R~~~P~~t~lIF~SGKivitGaks~~~~~~a~~~i~~   83 (99)
T d1qnaa1           5 IVPTLQNIVSTVNLDCKLDLKAIALQ-ARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYAR   83 (99)
T ss_dssp             CCCEEEEEEEEEECCSCCCHHHHHHH-CSSEEECTTTCSEEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEEEcCCcccHHHHHhh-CCCCEECcccCCEEEEEeCCCcEEEEEEcCCEEEEeccCCHHHHHHHHHHHHH
Confidence            35799999999999999999999975 88999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhc
Q 047239          171 VLNVY  175 (180)
Q Consensus       171 ~L~~~  175 (180)
                      +|.++
T Consensus        84 ~l~k~   88 (99)
T d1qnaa1          84 IVQKL   88 (99)
T ss_dssp             HHHHT
T ss_pred             HHHHc
Confidence            99875

>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=99.97  E-value=5.4e-31  Score=184.72  Aligned_cols=79  Identities=33%  Similarity=0.495  Sum_probs=76.3

Q ss_pred             EEEEEEEEcCCccCHHHHHhhC-CCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHc
Q 047239            6 QNIVATINLECKLDLKKIALHA-RNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKI   84 (180)
Q Consensus         6 ~NvVas~~l~~~ldL~~la~~~-~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~   84 (180)
                      ||||||++++++|||++||... .+++||||+||||+||+++|+++++||+||||+||||||++|++.|++++.++|+++
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            7999999999999999999875 589999999999999999999999999999999999999999999999999999876