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= 025357
(254 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1C9B|A Chain A, 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|E Chain E, 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|I Chain I, 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|M Chain M, 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|Q Chain Q, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
Length = 207
Score = 103 bits (257), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 50/94 (53%), Positives = 67/94 (71%), Gaps = 1/94 (1%)
Query: 103 DRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQ 162
DR ++ AFK I+ M+DR+ L I DR N ++K+V +QK L+GR +AI +ACLYIACRQ
Sbjct: 2 DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61
Query: 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
E PRT KE C+V+ +KKEIGR + I+K LE
Sbjct: 62 EGVPRTFKEICAVSR-ISKKEIGRCFKLILKALE 94
>pdb|1TFB|A Chain A, Nmr Studies Of Human General Transcription Factor Tfiib:
Dynamics And Interaction With Vp16 Activation Domain, 20
Structures
Length = 208
Score = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 49/93 (52%), Positives = 66/93 (70%), Gaps = 1/93 (1%)
Query: 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163
R ++ AFK I+ M+DR+ L I DR N ++K+V +QK L+GR +AI +ACLYIACRQE
Sbjct: 4 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 63
Query: 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
PRT KE C+V+ +KKEIGR + I+K LE
Sbjct: 64 GVPRTFKEICAVSR-ISKKEIGRCFKLILKALE 95
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib
Length = 206
Score = 101 bits (251), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 49/93 (52%), Positives = 66/93 (70%), Gaps = 1/93 (1%)
Query: 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163
R ++ AFK I+ M+DR+ L I DR N ++K+V +QK L+GR +AI +ACLYIACRQE
Sbjct: 2 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 61
Query: 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
PRT KE C+V+ +KKEIGR + I+K LE
Sbjct: 62 GVPRTFKEICAVSR-ISKKEIGRCFKLILKALE 93
>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
Length = 204
Score = 94.0 bits (232), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 45/91 (49%), Positives = 63/91 (69%), Gaps = 1/91 (1%)
Query: 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165
++ AFK I+ M+DR+ L DR N ++++ +QK L+GR +AI +ACLYIACRQE
Sbjct: 2 MMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGV 61
Query: 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196
PRT KE C+V+ +KKEIGR + I+K LE
Sbjct: 62 PRTFKEICAVSR-ISKKEIGRCFKLILKALE 91
>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|4BBR|M Chain M, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|M Chain M, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 345
Score = 87.0 bits (214), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 62/185 (33%), Positives = 85/185 (45%), Gaps = 7/185 (3%)
Query: 6 CADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDH---DPVRVXX 61
C +CK ++V S GD +C+ CGLVL VD SEWR F+N+ DH DP RV
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSND--DHNGDDPSRVGE 81
Query: 62 XXXXXXXXXXXXTVIAKPTAXXXXXXXXXXXXXXQARSSHPDRNLIQAFKSISAMSDRLG 121
T I K + D + AF I+ + D
Sbjct: 82 ASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAE 141
Query: 122 LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK 181
L +KD A E YK D+K L+G++ E+I+AA + I CR+ RT KE S+ + T
Sbjct: 142 LPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKT- 200
Query: 182 KEIGR 186
KE G+
Sbjct: 201 KEFGK 205
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
Box Complex From Pyrococcus Woesei
Length = 201
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 34/97 (35%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 99 SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
S +RNL A + ++ +L L +++ A +Y++ + +RGR+ E+++AAC+Y
Sbjct: 3 SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 62
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195
ACR PRT+ E +A KKEIGR+ FI ++L
Sbjct: 63 ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL 98
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 44/92 (47%)
Query: 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACR 161
P + ++ ++ +D LGL ++ RA EI + + G++ +VAA LYIA
Sbjct: 102 PKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASL 161
Query: 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193
E + RT +E VA T R KE + K
Sbjct: 162 LEGEKRTQREVAEVARVTEVTVRNRYKELVEK 193
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
Complex From Pyrococcus Woesei
Length = 200
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/97 (35%), Positives = 57/97 (58%), Gaps = 1/97 (1%)
Query: 99 SSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
S +RNL A + ++ +L L +++ A +Y++ + +RGR+ E+++AAC+Y
Sbjct: 2 SDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYA 61
Query: 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195
ACR PRT+ E +A KKEIGR+ FI ++L
Sbjct: 62 ACRLLKVPRTLDEIADIAR-VDKKEIGRSYRFIARNL 97
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 44/92 (47%)
Query: 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACR 161
P + ++ ++ +D LGL ++ RA EI + + G++ +VAA LYIA
Sbjct: 101 PKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASL 160
Query: 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193
E + RT +E VA T R KE + K
Sbjct: 161 LEGEKRTQREVAEVARVTEVTVRNRYKELVEK 192
>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human
General Transcription Tfiib (Zinc Bound Structures)
pdb|1RO4|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human
General Transcription Factor Tfiib (Zinc Free
Structures)
Length = 60
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 26/38 (68%)
Query: 15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESS 52
+V D+ AGD IC ECGLV+ +D SEWR F+N+ +
Sbjct: 23 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKA 60
>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain
Length = 58
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 15 VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANE 50
+V D+ AGD IC ECGLV+ +D SEWR F+N+
Sbjct: 22 LVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57
>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
Length = 197
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 6 CADCKRLT-EVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN 49
C +CK ++V S GD +C+ CGLVL VD SEWR F+N
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68
>pdb|1ZP2|A Chain A, Structure Of The Mediator Subunit Cyclin C
Length = 235
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 104 RNLIQAFKSISAMSDRLGL-----VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158
++ I +K + DRL L T I + KK E+ +G + EA+VA C+Y+
Sbjct: 26 KDTIYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEE----KGFSLEALVATCIYL 81
Query: 159 ACRQENKPRTVKEFCSVAN 177
+C+ E P ++ C+ AN
Sbjct: 82 SCKVEECPVHIRTICNEAN 100
>pdb|1PFT|A Chain A, N-Terminal Domain Of Tfiib, Nmr
Length = 50
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 13 TEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF 47
E+++D G+ +C++CG V+E +D EWR F
Sbjct: 14 AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48
>pdb|4HC7|A Chain A, Crystal Structure Of The Full Dna Binding Domain Of
Gata3-Complex 2
pdb|4HC7|B Chain B, Crystal Structure Of The Full Dna Binding Domain Of
Gata3-Complex 2
pdb|4HC9|A Chain A, Dna Binding By Gata Transcription Factor-Complex 3
pdb|4HCA|A Chain A, Dna Binding By Gata Transcription Factor-Complex 1
Length = 115
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 2 ADSYCADCKRLTEVVFDHSA-GDTICSECGLVLEAYSVDE 40
A + CA+C+ T ++ +A GD +C+ CGL + ++++
Sbjct: 58 AGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINR 97
>pdb|3DFV|D Chain D, Adjacent Gata Dna Binding
pdb|3DFV|C Chain C, Adjacent Gata Dna Binding
pdb|3DFX|A Chain A, Opposite Gata Dna Binding
pdb|3DFX|B Chain B, Opposite Gata Dna Binding
Length = 63
Score = 28.9 bits (63), Expect = 3.1, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 2 ADSYCADCKRLTEVVFDHSA-GDTICSECGLVLEAYSVD 39
A + CA+C+ T ++ +A GD +C+ CGL + ++++
Sbjct: 6 AGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNIN 44
>pdb|3GAT|A Chain A, Solution Nmr Structure Of The C-Terminal Domain Of
Chicken Gata-1 Bound To Dna, 34 Structures
pdb|2GAT|A Chain A, Solution Structure Of The C-Terminal Domain Of Chicken
Gata- 1 Bound To Dna, Nmr, Regularized Mean Structure
Length = 66
Score = 27.3 bits (59), Expect = 8.5, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 2 ADSYCADCKRLTEVVFDHSA-GDTICSECGLVLEAYSVD 39
A + C++C+ T ++ S GD +C+ CGL + + V+
Sbjct: 3 AGTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVN 41
>pdb|1GAT|A Chain A, Solution Structure Of The Specific Dna Complex Of The
Zinc Containing Dna Binding Domain Of The Erythroid
Transcription Factor Gata-1 By Multidimensional Nmr
pdb|1GAU|A Chain A, Solution Structure Of The Specific Dna Complex Of The
Zinc Containing Dna Binding Domain Of The Erythroid
Transcription Factor Gata-1 By Multidimensional Nmr
Length = 60
Score = 27.3 bits (59), Expect = 8.6, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 2 ADSYCADCKRLTEVVFDHSA-GDTICSECGLVLEAYSVD 39
A + C++C+ T ++ S GD +C+ CGL + + V+
Sbjct: 3 AGTVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVN 41
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
0.319 0.130 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,708,957
Number of Sequences: 62578
Number of extensions: 169419
Number of successful extensions: 353
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 327
Number of HSP's gapped (non-prelim): 24
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)