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= 008401
(567 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
Complex From Pyrococcus Woesei
Length = 200
Score = 82.4 bits (202), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 51/165 (30%), Positives = 87/165 (52%), Gaps = 11/165 (6%)
Query: 97 AKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 156
A R Y AV + +GR E V A+C+Y ACR P L + ++ ++ E+G Y
Sbjct: 33 AARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYR- 91
Query: 157 LCQVLYIADESNVLKQ---VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTG 213
+IA N+ + V P+ +++KF D L G ++KV A +IL + +T+G
Sbjct: 92 -----FIARNLNLTPKKLFVKPTDYVNKFADEL--GLSEKVRRRAIEILDEAYKRGLTSG 144
Query: 214 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258
+ P+GL AALY+++L G K ++ ++ ++ + E T+ R E
Sbjct: 145 KSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKEL 189
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
Box Complex From Pyrococcus Woesei
Length = 201
Score = 82.4 bits (202), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 51/165 (30%), Positives = 87/165 (52%), Gaps = 11/165 (6%)
Query: 97 AKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQ 156
A R Y AV + +GR E V A+C+Y ACR P L + ++ ++ E+G Y
Sbjct: 34 AARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYR- 92
Query: 157 LCQVLYIADESNVLKQ---VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTG 213
+IA N+ + V P+ +++KF D L G ++KV A +IL + +T+G
Sbjct: 93 -----FIARNLNLTPKKLFVKPTDYVNKFADEL--GLSEKVRRRAIEILDEAYKRGLTSG 145
Query: 214 RKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEATLMKRLIEF 258
+ P+GL AALY+++L G K ++ ++ ++ + E T+ R E
Sbjct: 146 KSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKEL 190
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 47/192 (24%), Positives = 87/192 (45%), Gaps = 13/192 (6%)
Query: 68 ERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC 127
+R M AF ++ M + +N+ + IV + + KGR + + ++CLY+AC
Sbjct: 2 DRAMMNAFKEITTMADRINLPRN--IVDRTNNLFKQVYEQKSLKGRANDAIASACLYIAC 59
Query: 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL- 186
RQ+ P + I+ E+G + + + L E++V + F+ +F L
Sbjct: 60 RQEGVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLC 114
Query: 187 LPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHI 246
LP K+V A I + GR P + AA+Y+++ K ++ +I I +
Sbjct: 115 LP---KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGV 171
Query: 247 CEATLMK--RLI 256
+ T+ + RLI
Sbjct: 172 ADVTIRQSYRLI 183
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib
Length = 206
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 47/191 (24%), Positives = 86/191 (45%), Gaps = 13/191 (6%)
Query: 69 RLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACR 128
R M AF ++ M + +N+ + IV + + KGR + + ++CLY+ACR
Sbjct: 2 RAMMNAFKEITTMADRINLPRN--IVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACR 59
Query: 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-L 187
Q+ P + I+ E+G + + + L E++V + F+ +F L L
Sbjct: 60 QEGVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCL 114
Query: 188 PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC 247
P K+V A I + GR P + AA+Y+++ K ++ +I I +
Sbjct: 115 P---KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVA 171
Query: 248 EATLMK--RLI 256
+ T+ + RLI
Sbjct: 172 DVTIRQSYRLI 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 = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 47/191 (24%), Positives = 86/191 (45%), Gaps = 13/191 (6%)
Query: 69 RLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACR 128
R M AF ++ M + +N+ + IV + + KGR + + ++CLY+ACR
Sbjct: 4 RAMMNAFKEITTMADRINLPRN--IVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACR 61
Query: 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-L 187
Q+ P + I+ E+G + + + L E++V + F+ +F L L
Sbjct: 62 QEGVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCL 116
Query: 188 PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHIC 247
P K+V A I + GR P + AA+Y+++ K ++ +I I +
Sbjct: 117 P---KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVA 173
Query: 248 EATLMK--RLI 256
+ T+ + RLI
Sbjct: 174 DVTIRQSYRLI 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 = 3e-05, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 13/189 (6%)
Query: 71 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQK 130
M AF ++ M + +N+ + V + A + KGR + + ++CLY+ACRQ+
Sbjct: 2 MMNAFKEITTMADRINLPRNK--VDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQE 59
Query: 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL-LPG 189
P + I+ E+G + + + L E++V + F+ +F L LP
Sbjct: 60 GVPRTFKEICAVSRISKKEIGRCFKLILKAL----ETSV-DLITTGDFMSRFCSNLCLP- 113
Query: 190 GNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIVKIVHICEA 249
K+V A I + GR P + AA+Y+++ K ++ +I I + +
Sbjct: 114 --KQVQMAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADV 171
Query: 250 TLMK--RLI 256
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 = 0.060, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 409 TEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREY 450
++ SD DN D+DD E++ +L NEE K+ IW +N ++
Sbjct: 19 SKVSDDPDNLEDVDDEELNAHLLNEEASKLKERIWIGLNADF 60
>pdb|1EIA|A Chain A, X-Ray Crystal Structure Of Equine Infectious Anemia Virus
(Eiav) Capsid Protein P26
Length = 207
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 38/96 (39%), Gaps = 10/96 (10%)
Query: 20 QLCCDRCGKVLEDHNFS---TEATFVKNAAGQSQLSGNFVRTIQSEYGASRERLMEKAFD 76
Q+ D K+ +D + A V G ++ F+R + G RER ME AFD
Sbjct: 53 QILLDAIDKIADDWDNRHPLPNAPLVAPPQGPIPMTARFIRGL----GVPRERQMEPAFD 108
Query: 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKG 112
RQ I E + V G A+N +G
Sbjct: 109 QFRQTYRQWIIEAMSEGIKV---MIGKPKAQNIRQG 141
>pdb|2EIA|A Chain A, X-Ray Crystal Structure Of Equine Infectious Anemia Virus
(Eiav) Capsid Protein P26
pdb|2EIA|B Chain B, X-Ray Crystal Structure Of Equine Infectious Anemia Virus
(Eiav) Capsid Protein P26
Length = 206
Score = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 38/96 (39%), Gaps = 10/96 (10%)
Query: 20 QLCCDRCGKVLEDHNFS---TEATFVKNAAGQSQLSGNFVRTIQSEYGASRERLMEKAFD 76
Q+ D K+ +D + A V G ++ F+R + G RER ME AFD
Sbjct: 52 QILLDAIDKIADDWDNRHPLPNAPLVAPPQGPIPMTARFIRGL----GVPRERQMEPAFD 107
Query: 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKG 112
RQ I E + V G A+N +G
Sbjct: 108 QFRQTYRQWIIEAMSEGIKV---MIGKPKAQNIRQG 140
>pdb|3MBO|A Chain A, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|B Chain B, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|C Chain C, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|D Chain D, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|E Chain E, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|F Chain F, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|G Chain G, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
pdb|3MBO|H Chain H, Crystal Structure Of The Glycosyltransferase Babsha Bound
With Udp And L-Malate
Length = 414
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 35/132 (26%), Positives = 56/132 (42%), Gaps = 22/132 (16%)
Query: 57 RTIQSEYGASRERLMEKAFDDMRQMKNALNIGESDEI-VHVAKRFYGIAVARNFTKGRRT 115
+ IQ+ Y ER+ K DM Q+K I ES++I +H++ NF K +R
Sbjct: 199 KDIQTVYNFIDERVYFKR--DMTQLKKEYGISESEKILIHIS----------NFRKVKRV 246
Query: 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDP 175
+ V + + +K L+ D + I LQL + L+I D L + D
Sbjct: 247 QDVVQAFAKIVTEVDAKLLLVGDGPEFCTI---------LQLVKNLHIEDRVLFLGKQDN 297
Query: 176 SIFLHKFTDRLL 187
L +D +L
Sbjct: 298 VAELLAMSDLML 309
>pdb|2JJM|A Chain A, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|B Chain B, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|C Chain C, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|D Chain D, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|E Chain E, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|F Chain F, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|G Chain G, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|H Chain H, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|I Chain I, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|J Chain J, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|K Chain K, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558.
pdb|2JJM|L Chain L, Crystal Structure Of A Family Gt4 Glycosyltransferase From
Bacillus Anthracis Orf Ba1558
Length = 394
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 35/132 (26%), Positives = 56/132 (42%), Gaps = 22/132 (16%)
Query: 57 RTIQSEYGASRERLMEKAFDDMRQMKNALNIGESDEI-VHVAKRFYGIAVARNFTKGRRT 115
+ IQ+ Y ER+ K DM Q+K I ES++I +H++ NF K +R
Sbjct: 179 KDIQTVYNFIDERVYFKR--DMTQLKKEYGISESEKILIHIS----------NFRKVKRV 226
Query: 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDP 175
+ V + + +K L+ D + I LQL + L+I D L + D
Sbjct: 227 QDVVQAFAKIVTEVDAKLLLVGDGPEFCTI---------LQLVKNLHIEDRVLFLGKQDN 277
Query: 176 SIFLHKFTDRLL 187
L +D +L
Sbjct: 278 VAELLAMSDLML 289
>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 = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 13/81 (16%)
Query: 231 HGLKFSKSDIVKIVHICEATLM-KRLIEFE---NTDSGSLTIEDFMARKKELHEGVAANL 286
HG+ SD K+ A +M K L+++E + D LT+ A EG L
Sbjct: 204 HGVAMLTSDPPKL----NAFIMDKSLLDYEVSIDADCKLLTVGKPFAI-----EGYGIGL 254
Query: 287 PNNGPKVSGMNEVLCKHKDTG 307
P N P S ++E + ++K +G
Sbjct: 255 PQNSPLTSNLSEFISRYKSSG 275
>pdb|2RC7|A Chain A, Crystal Structure Of The Nr3a Ligand Binding Core Complex
With Glycine At 1.58 Angstrom Resolution
pdb|2RC8|A Chain A, Crystal Structure Of The Nr3a Ligand Binding Core Complex
With D- Serine At 1.45 Angstrom Resolution
pdb|2RC8|B Chain B, Crystal Structure Of The Nr3a Ligand Binding Core Complex
With D- Serine At 1.45 Angstrom Resolution
pdb|2RC9|A Chain A, Crystal Structure Of The Nr3a Ligand Binding Core Complex
With Acpc At 1.96 Angstrom Resolution
pdb|2RC9|B Chain B, Crystal Structure Of The Nr3a Ligand Binding Core Complex
With Acpc At 1.96 Angstrom Resolution
pdb|2RC7|B Chain B, Crystal Structure Of The Nr3a Ligand Binding Core Complex
With Glycine At 1.58 Angstrom Resolution
Length = 294
Score = 28.5 bits (62), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 13/86 (15%)
Query: 226 VSALTHGLKFSKSDIVKIVHICEATLM-KRLIEFE---NTDSGSLTIEDFMARKKELHEG 281
V A G+++ K+D K+ +A +M K L+++E + D LT+ A EG
Sbjct: 201 VPATPDGVQYLKNDPEKL----DAFIMDKALLDYEVSIDADCKLLTVGKPFAI-----EG 251
Query: 282 VAANLPNNGPKVSGMNEVLCKHKDTG 307
LP N P S ++E++ ++K G
Sbjct: 252 YGIGLPPNSPLTSNISELISQYKSHG 277
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
0.317 0.132 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,422,533
Number of Sequences: 62578
Number of extensions: 604323
Number of successful extensions: 1371
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1346
Number of HSP's gapped (non-prelim): 29
length of query: 567
length of database: 14,973,337
effective HSP length: 104
effective length of query: 463
effective length of database: 8,465,225
effective search space: 3919399175
effective search space used: 3919399175
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)