BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 031013
(167 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VTO|A Chain A, 1.9 A Resolution Refined Structure Of Tbp Recognizing The
Minor Groove Of Tataaaag
pdb|1VTO|B Chain B, 1.9 A Resolution Refined Structure Of Tbp Recognizing The
Minor Groove Of Tataaaag
Length = 190
Score = 280 bits (715), Expect = 4e-76, Method: Compositional matrix adjust.
Identities = 141/181 (77%), Positives = 149/181 (82%), Gaps = 24/181 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK
Sbjct: 10 GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 69
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 70 VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 129
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+Q
Sbjct: 130 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 189
Query: 167 Q 167
Q
Sbjct: 190 Q 190
>pdb|1VOK|A Chain A, Arabidopsis Thaliana Tbp (Dimer)
pdb|1VOK|B Chain B, Arabidopsis Thaliana Tbp (Dimer)
pdb|1VOL|B Chain B, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
pdb|1QN5|A Chain A, Crystal Structure Of The G(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN5|B Chain B, Crystal Structure Of The G(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN6|A Chain A, Crystal Structure Of The T(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN6|B Chain B, Crystal Structure Of The T(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN7|A Chain A, Crystal Structure Of The T(-27) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN7|B Chain B, Crystal Structure Of The T(-27) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN8|A Chain A, Crystal Structure Of The T(-28) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN8|B Chain B, Crystal Structure Of The T(-28) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN9|A Chain A, Crystal Structure Of The C(-29) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN9|B Chain B, Crystal Structure Of The C(-29) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNA|A Chain A, Crystal Structure Of The T(-30) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNA|B Chain B, Crystal Structure Of The T(-30) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNB|A Chain A, Crystal Structure Of The T(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNB|B Chain B, Crystal Structure Of The T(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNC|A Chain A, Crystal Structure Of The A(-31) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNC|B Chain B, Crystal Structure Of The A(-31) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNE|A Chain A, Crystal Structure Of The Adenovirus Major Late Promoter
Tata Box Bound To Wild-Type Tbp (Arabidopsis Thaliana
Tbp Isoform 2).
pdb|1QNE|B Chain B, Crystal Structure Of The Adenovirus Major Late Promoter
Tata Box Bound To Wild-Type Tbp (Arabidopsis Thaliana
Tbp Isoform 2).
pdb|1QN3|A Chain A, Crystal Structure Of The C(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN3|B Chain B, Crystal Structure Of The C(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN4|A Chain A, Crystal Structure Of The T(-24) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN4|B Chain B, Crystal Structure Of The T(-24) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution
Length = 200
Score = 280 bits (715), Expect = 4e-76, Method: Compositional matrix adjust.
Identities = 141/181 (77%), Positives = 149/181 (82%), Gaps = 24/181 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK
Sbjct: 20 GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 79
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 80 VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 139
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKVQ 166
FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+Q
Sbjct: 140 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 199
Query: 167 Q 167
Q
Sbjct: 200 Q 200
>pdb|1VTL|E Chain E, Co-Crystal Structure Of Tbp Recognizing The Minor Groove
Of A Tata Element
pdb|1VTL|F Chain F, Co-Crystal Structure Of Tbp Recognizing The Minor Groove
Of A Tata Element
Length = 186
Score = 275 bits (704), Expect = 7e-75, Method: Compositional matrix adjust.
Identities = 139/179 (77%), Positives = 147/179 (82%), Gaps = 24/179 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V +++NIVSTVNLDCKLDLK IALQARNAEYNPK
Sbjct: 8 GIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 67
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE SK+AARKYARI+QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSH A
Sbjct: 68 VCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA 127
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
FSSYEPELFPGLIYRMK PKIVLLIFVSGKIVITGAK+RDETY AFENIYPVL+EFRK+
Sbjct: 128 FSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 186
>pdb|1JFI|C Chain C, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 185
Score = 248 bits (634), Expect = 9e-67, Method: Compositional matrix adjust.
Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V ++NIVSTVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 6 GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 65
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL +H
Sbjct: 66 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 125
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L FRK
Sbjct: 126 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 183
>pdb|1NVP|A Chain A, Human TfiiaTBPDNA COMPLEX
Length = 181
Score = 248 bits (633), Expect = 1e-66, Method: Compositional matrix adjust.
Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V ++NIVSTVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 2 GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 61
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL +H
Sbjct: 62 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 121
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L FRK
Sbjct: 122 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 179
>pdb|1TGH|A Chain A, Tata Binding Protein (Tbp)DNA COMPLEX
Length = 185
Score = 248 bits (632), Expect = 1e-66, Method: Compositional matrix adjust.
Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V ++NIVSTVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 6 GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 65
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL +H
Sbjct: 66 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 125
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L FRK
Sbjct: 126 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 183
>pdb|1C9B|B Chain B, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|F Chain F, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|J Chain J, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|N Chain N, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|R Chain R, 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
Score = 248 bits (632), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 124/178 (69%), Positives = 138/178 (77%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V ++NIVSTVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 3 GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 62
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE+QS+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL +H
Sbjct: 63 VCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 122
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L FRK
Sbjct: 123 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 180
>pdb|1TBP|A Chain A, Crystal Structure Of Yeast Tata-Binding Protein And Model
For Interaction With Dna
pdb|1TBP|B Chain B, Crystal Structure Of Yeast Tata-Binding Protein And Model
For Interaction With Dna
Length = 180
Score = 248 bits (632), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 124/180 (68%), Positives = 139/180 (77%), Gaps = 24/180 (13%)
Query: 10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK----------------------- 46
+G V +++NIV+TV L C+LDLK +AL ARNAEYNPK
Sbjct: 1 MGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK 60
Query: 47 -VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHG 105
V TGAKSE SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG
Sbjct: 61 MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG 120
Query: 106 AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
FSSYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 121 TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 180
>pdb|1RM1|A Chain A, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex
Length = 240
Score = 247 bits (630), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 124/179 (69%), Positives = 138/179 (77%), Gaps = 24/179 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V +++NIV+TV L C+LDLK +AL ARNAEYNPK
Sbjct: 62 GIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 121
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
V TGAKSE SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG
Sbjct: 122 VVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGT 181
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
FSSYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 182 FSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 240
>pdb|1YTB|A Chain A, Crystal Structure Of A Yeast TbpTATA-Box Complex
pdb|1YTB|B Chain B, Crystal Structure Of A Yeast TbpTATA-Box Complex
pdb|1YTF|A Chain A, Yeast TfiiaTBPDNA COMPLEX
pdb|1TBA|B Chain B, Solution Structure Of A Tbp-Tafii230 Complex: Protein
Mimicry Of The Minor Groove Surface Of The Tata Box
Unwound By Tbp, Nmr, 25 Structures
pdb|1NGM|A Chain A, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NGM|E Chain E, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NGM|I Chain I, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NGM|M Chain M, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NH2|A Chain A, Crystal Structure Of A Yeast TfiiaTBPDNA COMPLEX
Length = 180
Score = 246 bits (629), Expect = 4e-66, Method: Compositional matrix adjust.
Identities = 124/179 (69%), Positives = 138/179 (77%), Gaps = 24/179 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V +++NIV+TV L C+LDLK +AL ARNAEYNPK
Sbjct: 2 GIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 61
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
V TGAKSE SKLA+RKYARIIQK+GF AKF DFKIQNIVGSCDVKFPIRLEGLA+SHG
Sbjct: 62 VVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGT 121
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
FSSYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAK R+E Y AFE IYPVL+EFRK+
Sbjct: 122 FSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 180
>pdb|1CDW|A Chain A, Human Tbp Core Domain Complexed With Dna
Length = 179
Score = 246 bits (627), Expect = 6e-66, Method: Compositional matrix adjust.
Identities = 123/178 (69%), Positives = 137/178 (76%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G V ++NIVSTVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 2 GIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKM 61
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
VCTGAKSE+ S+LAARKYAR++QKLGFPAKF DFKIQN+VGSCDVKFPIRLEGL +H
Sbjct: 62 VCTGAKSEENSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQ 121
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
FSSYEPELFPGLIYRM +P+IVLLIFVSGK+V+TGAKVR E Y AFENIYP+L FRK
Sbjct: 122 FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 179
>pdb|3OC3|C Chain C, Crystal Structure Of The Mot1 N-Terminal Domain In Complex
With Tbp
pdb|3OC3|D Chain D, Crystal Structure Of The Mot1 N-Terminal Domain In Complex
With Tbp
pdb|3OCI|A Chain A, Crystal Structure Of Tbp (Tata Box Binding Protein)
pdb|3OCI|B Chain B, Crystal Structure Of Tbp (Tata Box Binding Protein)
Length = 218
Score = 228 bits (581), Expect = 1e-60, Method: Compositional matrix adjust.
Identities = 113/178 (63%), Positives = 133/178 (74%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G + +++N+V+TVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 40 GIIPTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 99
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
V TGAKSE+ S++AA++YA+II KLGF A F DFKIQNIV SCD+KF IRLEGLAY+H
Sbjct: 100 VITGAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSN 159
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
+ SYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAKVRD+ Y AF NIYPVL + RK
Sbjct: 160 YCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVLIQHRK 217
>pdb|3EIK|A Chain A, Double Stranded Dna Binding Protein
pdb|3EIK|B Chain B, Double Stranded Dna Binding Protein
Length = 218
Score = 228 bits (581), Expect = 1e-60, Method: Compositional matrix adjust.
Identities = 113/178 (63%), Positives = 133/178 (74%), Gaps = 24/178 (13%)
Query: 11 GAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------ 46
G + +++N+V+TVNL CKLDLK IAL+ARNAEYNPK
Sbjct: 40 GIIPTLQNVVATVNLSCKLDLKNIALRARNAEYNPKRFAAVIMRIREPKTTALIFASGKM 99
Query: 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
V TGAKSE+ S++AA++YA+II KLGF A F DFKIQNIV SCD+KF IRLEGLAY+H
Sbjct: 100 VITGAKSEKSSRMAAQRYAKIIHKLGFNATFDDFKIQNIVSSCDIKFSIRLEGLAYAHSN 159
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164
+ SYEPELFPGLIYRM +PKIVLLIFVSGKIV+TGAKVRD+ Y AF NIYPVL + RK
Sbjct: 160 YCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYPVLIQHRK 217
>pdb|1MP9|A Chain A, Tbp From A Mesothermophilic Archaeon, Sulfolobus
Acidocaldarius
pdb|1MP9|B Chain B, Tbp From A Mesothermophilic Archaeon, Sulfolobus
Acidocaldarius
Length = 198
Score = 105 bits (261), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 67/176 (38%), Positives = 93/176 (52%), Gaps = 26/176 (14%)
Query: 12 AVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------V 47
AV +++NIV+TV LD LDL + N EY+P V
Sbjct: 11 AVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMV 70
Query: 48 CTGAKSEQQSKLAARKYARIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHGA 106
TGAKS + A ++ + ++K G K +IQNIV S ++ + L+ A+
Sbjct: 71 VTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLEN 130
Query: 107 FSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
+ YEPE FPGLIYRM +P++VLLIF SGK+VITGAK DE + A + I+ L E
Sbjct: 131 -NMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVEL 185
>pdb|2Z8U|A Chain A, Methanococcus Jannaschii Tbp
pdb|2Z8U|B Chain B, Methanococcus Jannaschii Tbp
pdb|2Z8U|P Chain P, Methanococcus Jannaschii Tbp
pdb|2Z8U|Q Chain Q, Methanococcus Jannaschii Tbp
Length = 188
Score = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 54/173 (31%), Positives = 93/173 (53%), Gaps = 26/173 (15%)
Query: 18 NIVSTVNLDCKLDLKKIALQARNAEYNPKV------------------------CTGAKS 53
N+V + + +DL+++A+ NAEY P+ CTGAKS
Sbjct: 17 NVVVSTKIGDNIDLEEVAMILENAEYEPEQFPGLVCRLSVPKVALLIFRSGKVNCTGAKS 76
Query: 54 EQQSKLAARKYARIIQKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEP 112
++++++A +K + ++ G + + KIQN+V + D+ L+ +A + YEP
Sbjct: 77 KEEAEIAIKKIIKELKDAGIDVIENPEIKIQNMVATADLGIEPNLDDIALMVEG-TEYEP 135
Query: 113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165
E FPGL+YR+ PK+V+LIF SGK+VITG K ++ A + I + E +++
Sbjct: 136 EQFPGLVYRLDDPKVVVLIFGSGKVVITGLKSEEDAKRALKKILDTIKEVQEL 188
>pdb|1AIS|A Chain A, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
Complex From Pyrococcus Woesei
Length = 182
Score = 86.3 bits (212), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 60/174 (34%), Positives = 93/174 (53%), Gaps = 30/174 (17%)
Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
++NIV++V+L +LDL+K+ N++YNP+ V TGA
Sbjct: 11 IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 52 KSEQQSKLAARKYARIIQKLGFPAKFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
KS Q + A K A+ ++ +G KFK +QN+V S D+ L+ +A +
Sbjct: 71 KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPN-C 127
Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
YEPE FPG+IYR+K+PK V+L+F SGKIV +GAK + + A + L ++
Sbjct: 128 EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181
>pdb|1PCZ|A Chain A, Structure Of Tata-Binding Protein
pdb|1PCZ|B Chain B, Structure Of Tata-Binding Protein
Length = 191
Score = 86.3 bits (212), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 60/174 (34%), Positives = 93/174 (53%), Gaps = 30/174 (17%)
Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
++NIV++V+L +LDL+K+ N++YNP+ V TGA
Sbjct: 11 IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 52 KSEQQSKLAARKYARIIQKLGFPAKFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
KS Q + A K A+ ++ +G KFK +QN+V S D+ L+ +A +
Sbjct: 71 KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPN-C 127
Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
YEPE FPG+IYR+K+PK V+L+F SGKIV +GAK + + A + L ++
Sbjct: 128 EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181
>pdb|1D3U|A Chain A, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
Box Complex From Pyrococcus Woesei
Length = 181
Score = 86.3 bits (212), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 60/174 (34%), Positives = 93/174 (53%), Gaps = 30/174 (17%)
Query: 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGA 51
++NIV++V+L +LDL+K+ N++YNP+ V TGA
Sbjct: 11 IENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGA 70
Query: 52 KSEQQSKLAARKYARIIQKLGFPAKFK---DFKIQNIVGSCDVKFPIRLEGLAYSHGAFS 108
KS Q + A K A+ ++ +G KFK +QN+V S D+ L+ +A +
Sbjct: 71 KSVQDIERAVAKLAQKLKSIG--VKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPN-C 127
Query: 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEF 162
YEPE FPG+IYR+K+PK V+L+F SGKIV +GAK + + A + L ++
Sbjct: 128 EYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY 181
>pdb|2JVF|A Chain A, Solution Structure Of M7, A Computationally-Designed
Artificial Protein
Length = 96
Score = 31.6 bits (70), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 38 ARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRL 97
AR N ++ A++++Q+K AR++QKLG +KD ++ V +VK +R+
Sbjct: 43 ARAGARNVQITISAENDEQAKELLELIARLLQKLG----YKDINVR--VNGTEVKIEVRV 96
>pdb|3ASM|A Chain A, Crystal Structure Of Q54a Mutant Protein Of Bst-Rnase Hiii
Length = 310
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 101 AYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148
A+ GA S P G ++ +K+P +V+ + SGK++ G E
Sbjct: 18 AHYEGALSDRLP---AGALFAVKRPDVVITAYRSGKVLFAGKAAEQEA 62
>pdb|2D0A|A Chain A, Crystal Structure Of Bst-Rnase Hiii
pdb|2D0B|A Chain A, Crystal Structure Of Bst-Rnase Hiii In Complex With Mg2+
pdb|2D0C|A Chain A, Crystal Structure Of Bst-Rnase Hiii In Complex With Mn2+
Length = 310
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 101 AYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148
A+ GA S P G ++ +K+P +V+ + SGK++ G E
Sbjct: 18 AHYEGALSDRLP---AGALFAVKRPDVVITAYRSGKVLFQGKAAEQEA 62
>pdb|1R6A|A Chain A, Structure Of The Dengue Virus 2'o Methyltransferase In
Complex With S-Adenosyl Homocysteine And Ribavirin 5'
Triphosphate
Length = 295
Score = 27.3 bits (59), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 18 NIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKS 53
NIVS+VN+ ++ + + ++ + A Y P V G+ +
Sbjct: 226 NIVSSVNMISRMLINRFTMRHKKATYEPDVDLGSGT 261
>pdb|1L9K|A Chain A, Dengue Methyltransferase
pdb|2P1D|A Chain A, Crystal Structure Of Dengue Methyltransferase In Complex
With Gtp And S-Adenosyl-L-Homocysteine
pdb|2P3L|A Chain A, Crystal Structure Of Dengue Methyltransferase In Complex
With Gpppa And S-Adenosyl-L-Homocysteine
pdb|2P3O|A Chain A, Crystal Structure Of Dengue Methyltransferase In Complex
With 7megpppa And S-adenosyl-l-homocysteine
pdb|2P3Q|A Chain A, Crystal Structure Of Dengue Methyltransferase In Complex
With Gpppg And S-Adenosyl-L-Homocysteine
pdb|2P40|A Chain A, Crystal Structure Of Dengue Methyltransferase In Complex
With 7megpppg
pdb|2P41|A Chain A, Crystal Structure Of Dengue Methyltransferase In Complex
With 7megpppg2'ome And S-Adenosyl-L-Homocysteine
Length = 305
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 18 NIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKS 53
NIVS+VN+ ++ + + ++ + A Y P V G+ +
Sbjct: 236 NIVSSVNMISRMLINRFTMRHKKATYEPDVDLGSGT 271
>pdb|3FHH|A Chain A, Crystal Structure Of The HemeHEMOGLOBIN OUTER MEMBRANE
Transporter Shua From Shigella Dysenteriae
Length = 640
Score = 26.9 bits (58), Expect = 5.6, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 23 VNLDCKLDLKKIALQARN----AEYNPKVCTGAKSEQQSKLAARKYA 65
+N D K+ ++ + A+N EY ++ GA+ E +S L A +A
Sbjct: 263 LNADAKIYWSEVRINAQNTGSSGEYREQITKGARLENRSTLFADSFA 309
>pdb|3N23|B Chain B, Crystal Structure Of The High Affinity Complex Between
Ouabain And The E2p Form Of The Sodium-Potassium Pump
pdb|3N23|D Chain D, Crystal Structure Of The High Affinity Complex Between
Ouabain And The E2p Form Of The Sodium-Potassium Pump
pdb|3N2F|B Chain B, Crystal Structure Of The Sodium-Potassium Pump
pdb|3N2F|D Chain D, Crystal Structure Of The Sodium-Potassium Pump
Length = 277
Score = 26.6 bits (57), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 42 EYNPKV----CTGAKSEQQSKLAARKYARIIQKLGFPAKF 77
+YNP V CTG + E + K+ +Y + GFP ++
Sbjct: 177 KYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPLQY 216
>pdb|3EVG|A Chain A, Crystal Structure Of Dengue-2 Virus Methyltransferase
Complexed With S-Adenosyl-L-Homocysteine
Length = 275
Score = 26.6 bits (57), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 18 NIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQ 55
NIVS+VN+ ++ + + ++ + A Y P V G+ +
Sbjct: 227 NIVSSVNMISRMLINRFTMRYKKATYEPDVDLGSGTRN 264
>pdb|3KDP|B Chain B, Crystal Structure Of The Sodium-potassium Pump
pdb|3KDP|D Chain D, Crystal Structure Of The Sodium-potassium Pump
Length = 286
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 42 EYNPKV----CTGAKSEQQSKLAARKYARIIQKLGFPAKF 77
+YNP V CTG + E + K+ +Y + GFP ++
Sbjct: 186 KYNPYVLPVHCTGKRDEDKEKVGTMEYFGLGGYPGFPLQY 225
>pdb|3BBC|A Chain A, Crystal Structure Of R88a Mutant Of The Nm23-H2
Transcription Factor
pdb|3BBC|B Chain B, Crystal Structure Of R88a Mutant Of The Nm23-H2
Transcription Factor
pdb|3BBC|C Chain C, Crystal Structure Of R88a Mutant Of The Nm23-H2
Transcription Factor
pdb|3BBC|D Chain D, Crystal Structure Of R88a Mutant Of The Nm23-H2
Transcription Factor
pdb|3BBC|E Chain E, Crystal Structure Of R88a Mutant Of The Nm23-H2
Transcription Factor
pdb|3BBC|F Chain F, Crystal Structure Of R88a Mutant Of The Nm23-H2
Transcription Factor
Length = 151
Score = 26.6 bits (57), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 114 LFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTA 151
FPGL+ M +V +++ +V TGA + ET A
Sbjct: 59 FFPGLVKYMNSGPVVAMVWEGLNVVKTGAVMLGETNPA 96
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.139 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,458,644
Number of Sequences: 62578
Number of extensions: 163375
Number of successful extensions: 286
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 216
Number of HSP's gapped (non-prelim): 30
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)