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= 010919
(497 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
Box Complex From Pyrococcus Woesei
Length = 201
Score = 82.8 bits (203), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 51/165 (30%), Positives = 87/165 (52%), Gaps = 11/165 (6%)
Query: 27 AKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 86
A R Y AV + +GR E V A+C+Y ACR P L + ++ ++ E+G Y
Sbjct: 34 AARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYR- 92
Query: 87 LCQVLYIADESNVLKQ---VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTG 143
+IA N+ + V P+ +++KF D L G ++KV A +IL + +T+G
Sbjct: 93 -----FIARNLNLTPKKLFVKPTDYVNKFADEL--GLSEKVRRRAIEILDEAYKRGLTSG 145
Query: 144 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188
+ P+GL AALY+++L G K ++ ++ ++ + E T+ R E
Sbjct: 146 KSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKEL 190
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
Complex From Pyrococcus Woesei
Length = 200
Score = 82.8 bits (203), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 51/165 (30%), Positives = 87/165 (52%), Gaps = 11/165 (6%)
Query: 27 AKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 86
A R Y AV + +GR E V A+C+Y ACR P L + ++ ++ E+G Y
Sbjct: 33 AARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYR- 91
Query: 87 LCQVLYIADESNVLKQ---VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTG 143
+IA N+ + V P+ +++KF D L G ++KV A +IL + +T+G
Sbjct: 92 -----FIARNLNLTPKKLFVKPTDYVNKFADEL--GLSEKVRRRAIEILDEAYKRGLTSG 144
Query: 144 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 188
+ P+GL AALY+++L G K ++ ++ ++ + E T+ R E
Sbjct: 145 KSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKEL 189
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 13/189 (6%)
Query: 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK 60
M AF ++ M + +N+ + IV + + KGR + + ++CLY+ACRQ+
Sbjct: 5 MMNAFKEITTMADRINLPRN--IVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 62
Query: 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPG 119
P + I+ E+G + + + L E++V + F+ +F L LP
Sbjct: 63 GVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCLP- 116
Query: 120 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA 179
K+V A I + GR P + AA+Y+++ K ++ +I I + +
Sbjct: 117 --KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 174
Query: 180 TLMK--RLI 186
T+ + RLI
Sbjct: 175 TIRQSYRLI 183
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib
Length = 206
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 13/189 (6%)
Query: 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK 60
M AF ++ M + +N+ + IV + + KGR + + ++CLY+ACRQ+
Sbjct: 4 MMNAFKEITTMADRINLPRN--IVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 61
Query: 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPG 119
P + I+ E+G + + + L E++V + F+ +F L LP
Sbjct: 62 GVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCLP- 115
Query: 120 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA 179
K+V A I + GR P + AA+Y+++ K ++ +I I + +
Sbjct: 116 --KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 173
Query: 180 TLMK--RLI 186
T+ + RLI
Sbjct: 174 TIRQSYRLI 182
>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 = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 13/189 (6%)
Query: 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK 60
M AF ++ M + +N+ + IV + + KGR + + ++CLY+ACRQ+
Sbjct: 6 MMNAFKEITTMADRINLPRN--IVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 63
Query: 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPG 119
P + I+ E+G + + + L E++V + F+ +F L LP
Sbjct: 64 GVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCLP- 117
Query: 120 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA 179
K+V A I + GR P + AA+Y+++ K ++ +I I + +
Sbjct: 118 --KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 175
Query: 180 TLMK--RLI 186
T+ + RLI
Sbjct: 176 TIRQSYRLI 184
>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
Length = 204
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 13/189 (6%)
Query: 1 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK 60
M AF ++ M + +N+ + V + A + KGR + + ++CLY+ACRQ+
Sbjct: 2 MMNAFKEITTMADRINLPRNK--VDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQE 59
Query: 61 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPG 119
P + I+ E+G + + + L E++V + F+ +F L LP
Sbjct: 60 GVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCLP- 113
Query: 120 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA 179
K+V A I + GR P + AA+Y+++ K ++ +I I + +
Sbjct: 114 --KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 171
Query: 180 TLMK--RLI 186
T+ + RLI
Sbjct: 172 TIRQSYRLI 180
>pdb|1NGM|B Chain B, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NGM|F Chain F, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NGM|J Chain J, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
pdb|1NGM|N Chain N, Crystal Structure Of A Yeast Brf1-Tbp-Dna Ternary Complex
Length = 72
Score = 35.8 bits (81), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 339 TEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREY 380
++ SD DN D+DD E++ +L NEE K+ IW +N ++
Sbjct: 19 SKVSDDPDNLEDVDDEELNAHLLNEEASKLKERIWIGLNADF 60
>pdb|2RCA|B Chain B, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With Glycine At 1.58 Angstrom Resolution
pdb|2RCB|A Chain A, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With D- Serine At 1.62 Angstrom Resolution
pdb|2RCB|B Chain B, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With D- Serine At 1.62 Angstrom Resolution
pdb|2RCA|A Chain A, Crystal Structure Of The Nr3b Ligand Binding Core Complex
With Glycine At 1.58 Angstrom Resolution
Length = 292
Score = 28.9 bits (63), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 13/81 (16%)
Query: 161 HGLKFSKSDIVKIVHICEATLM-KRLIEFE---NTDSGSLTIEDFMARKKELHEGVAANL 216
HG+ SD K+ A +M K L+++E + D LT+ A EG L
Sbjct: 204 HGVAMLTSDPPKL----NAFIMDKSLLDYEVSIDADCKLLTVGKPFAI-----EGYGIGL 254
Query: 217 PNNGPKVSGMNEVLCKHKDTG 237
P N P S ++E + ++K +G
Sbjct: 255 PQNSPLTSNLSEFISRYKSSG 275
>pdb|3GKE|A Chain A, Crystal Structure Of Dicamba Monooxygenase
pdb|3GKE|B Chain B, Crystal Structure Of Dicamba Monooxygenase
pdb|3GKE|C Chain C, Crystal Structure Of Dicamba Monooxygenase
pdb|3GB4|A Chain A, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Cobalt And Dicamba
pdb|3GB4|B Chain B, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Cobalt And Dicamba
pdb|3GB4|C Chain C, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Cobalt And Dicamba
pdb|3GOB|A Chain A, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Cobalt And Dcsa
pdb|3GOB|B Chain B, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Cobalt And Dcsa
pdb|3GOB|C Chain C, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Cobalt And Dcsa
pdb|3GTE|A Chain A, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Iron
pdb|3GTE|B Chain B, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Iron
pdb|3GTE|C Chain C, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Iron
pdb|3GTS|A Chain A, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Iron And Dicamba
pdb|3GTS|B Chain B, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Iron And Dicamba
pdb|3GTS|C Chain C, Crystal Structure Of Dicamba Monooxygenase With Non-Heme
Iron And Dicamba
pdb|3GL0|A Chain A, Crystal Structure Of Dicamba Monooxygenase Bound To 3,6
Dichlorosalicylic Acid (Dcsa)
pdb|3GL0|B Chain B, Crystal Structure Of Dicamba Monooxygenase Bound To 3,6
Dichlorosalicylic Acid (Dcsa)
pdb|3GL0|C Chain C, Crystal Structure Of Dicamba Monooxygenase Bound To 3,6
Dichlorosalicylic Acid (Dcsa)
pdb|3GL2|A Chain A, Crystal Structure Of Dicamba Monooxygenase Bound To
Dicamba
pdb|3GL2|B Chain B, Crystal Structure Of Dicamba Monooxygenase Bound To
Dicamba
pdb|3GL2|C Chain C, Crystal Structure Of Dicamba Monooxygenase Bound To
Dicamba
Length = 349
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 26/61 (42%)
Query: 310 IGVPKNCTTQTASNEGEGDHTKTPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYK 369
I V T + S G H TP +A+ GS IDD E+DG L + + +
Sbjct: 232 IAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALV 291
Query: 370 K 370
K
Sbjct: 292 K 292
>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 = 28.5 bits (62), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 28/163 (17%), Positives = 62/163 (38%), Gaps = 11/163 (6%)
Query: 27 AKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 86
AK Y + KG+ E + A+ + + CR+ + + +++ E G
Sbjct: 150 AKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLIHVKTKEFGKTLNI 209
Query: 87 LCQVLYIADESNVLKQVDPS--------IFLHKFTDRLLPGGNKKVCDTARDILASMKRD 138
+ +L E LK +D ++ +F L G +V +A K
Sbjct: 210 MKNILRGKSEDGFLK-IDTDNMSGAQNLTYIPRFCSHL--GLPMQVTTSAEYTAKKCKEI 266
Query: 139 WITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATL 181
G+ P + ++Y++ L + + + + + + + E T+
Sbjct: 267 KEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTI 309
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
0.316 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,404,919
Number of Sequences: 62578
Number of extensions: 529013
Number of successful extensions: 1220
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1195
Number of HSP's gapped (non-prelim): 25
length of query: 497
length of database: 14,973,337
effective HSP length: 103
effective length of query: 394
effective length of database: 8,527,803
effective search space: 3359954382
effective search space used: 3359954382
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)