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= 023958
(275 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OS6|A Chain A, Crystal Structure Of Putative
2,3-Dihydroxybenzoate-Specific Isochorismate Synthase,
Dhbc From Bacillus Anthracis.
pdb|3OS6|B Chain B, Crystal Structure Of Putative
2,3-Dihydroxybenzoate-Specific Isochorismate Synthase,
Dhbc From Bacillus Anthracis.
pdb|3OS6|C Chain C, Crystal Structure Of Putative
2,3-Dihydroxybenzoate-Specific Isochorismate Synthase,
Dhbc From Bacillus Anthracis.
pdb|3OS6|D Chain D, Crystal Structure Of Putative
2,3-Dihydroxybenzoate-Specific Isochorismate Synthase,
Dhbc From Bacillus Anthracis
Length = 399
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 40 IKALKKTDKNKLYNDVVEDNRAGFVFVKGFRVDDNESASAI 80
+K+ K DK KL ++ E N+ G+ F D+NE++ +
Sbjct: 151 VKSSGKIDKQKLLRELAEHNKHGYTFAVNLPKDENENSKTL 191
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 47/114 (41%), Gaps = 16/114 (14%)
Query: 109 NQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEA---LAF-VGDVQDAARFISPDN 164
+QR E D + + +++ EH+G H IEEA L F V D P
Sbjct: 255 SQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQA 314
Query: 165 LY--GSPVSPSGQNFAAPEGRMCNGLIHALISSFDFAKKT-------LKLDQVG 209
L G PV EGR+ L+ + DF+ +T L+LDQVG
Sbjct: 315 LQKSGRPVKSIRARLKGKEGRIRGNLMGKRV---DFSARTVISGDPNLELDQVG 365
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 47/114 (41%), Gaps = 16/114 (14%)
Query: 109 NQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEA---LAF-VGDVQDAARFISPDN 164
+QR E D + + +++ EH+G H IEEA L F V D P
Sbjct: 255 SQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQA 314
Query: 165 LY--GSPVSPSGQNFAAPEGRMCNGLIHALISSFDFAKKT-------LKLDQVG 209
L G PV EGR+ L+ + DF+ +T L+LDQVG
Sbjct: 315 LQKSGRPVKSIRARLKGKEGRIRGNLMGKRV---DFSARTVISGDPNLELDQVG 365
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 47/114 (41%), Gaps = 16/114 (14%)
Query: 109 NQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEA---LAF-VGDVQDAARFISPDN 164
+QR E D + + +++ EH+G H IEEA L F V D P
Sbjct: 255 SQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQA 314
Query: 165 LY--GSPVSPSGQNFAAPEGRMCNGLIHALISSFDFAKKT-------LKLDQVG 209
L G PV EGR+ L+ + DF+ +T L+LDQVG
Sbjct: 315 LQKSGRPVKSIRARLKGKEGRIRGNLMGKRV---DFSARTVISGDPNLELDQVG 365
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 15 EKI-WDLHDKLSDA-------IHSISRTHFLNSIKALKKTDKNKLYNDVV---EDNRAGF 63
EKI WDL + LS H ++R L ++++L+ D+N + VV ED GF
Sbjct: 637 EKIAWDLKNLLSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGF 696
Query: 64 VF 65
V
Sbjct: 697 VL 698
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 15 EKI-WDLHDKLSDA-------IHSISRTHFLNSIKALKKTDKNKLYNDVV---EDNRAGF 63
EKI WDL + LS H ++R L ++++L+ D+N + VV ED GF
Sbjct: 637 EKIAWDLKNLLSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGF 696
Query: 64 V 64
V
Sbjct: 697 V 697
>pdb|2ZKR|HH Chain h, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 214
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 175 QNFAAPEGRMCNGLIHALISSFDFAKKTLKLDQ 207
+N P+ R C G+ A I FD +K K+D+
Sbjct: 13 KNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDE 45
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
0.315 0.129 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,399,777
Number of Sequences: 62578
Number of extensions: 272375
Number of successful extensions: 814
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 812
Number of HSP's gapped (non-prelim): 10
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
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: 51 (24.3 bits)