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= 020252
(328 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
Length = 332
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 38/122 (31%), Positives = 60/122 (49%), Gaps = 15/122 (12%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
SDP+R LLT EE+ L+ G++ + KL E +REV+ + G
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDL 315
+ + +EL+R L+ G + +I +N+RLV+SIAK Y G G++ DL
Sbjct: 62 TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 121
Query: 316 VQ 317
+Q
Sbjct: 122 IQ 123
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/140 (29%), Positives = 65/140 (46%), Gaps = 30/140 (21%)
Query: 208 VDYSDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSER 255
V SDP+R LLT EE+ L+ G++ + KL E +REV+ +
Sbjct: 90 VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 149
Query: 256 CGGS------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRL 297
G+ P + V++ +EL+R L+ G + +I +N+RL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 298 VISIAKNYQGAGMNLQDLVQ 317
V+SIAK Y G G++ DL+Q
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQ 229
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 30/137 (21%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
SDP+R LLT EE+ L+ G++ + KL E +REV+ + G
Sbjct: 6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
+ P + V++ +EL+R L+ G + +I +N+RLV+S
Sbjct: 66 TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 125
Query: 301 IAKNYQGAGMNLQDLVQ 317
IAK Y G G++ DL+Q
Sbjct: 126 IAKKYTGRGLSFLDLIQ 142
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 30/137 (21%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
SDP+R LLT EE+ L+ G++ + KL E +REV+ + G
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
+ P + V++ +EL+R L+ G + +I +N+RLV+S
Sbjct: 62 TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 121
Query: 301 IAKNYQGAGMNLQDLVQ 317
IAK Y G G++ DL+Q
Sbjct: 122 IAKKYTGRGLSFLDLIQ 138
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
Length = 179
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 3/47 (6%)
Query: 274 RELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+EL+R L+ G + +I +N+RLV+SIAK Y G G++ DL+Q
Sbjct: 91 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 137
>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
Length = 423
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
G + +I +N+RLV+SIAK Y G G++ DL+Q
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214
>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
Length = 423
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
G + +I +N+RLV+SIAK Y G G++ DL+Q
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 443
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
G + +I +N+RLV+SIAK Y G G++ DL+Q
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 234
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 613
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297
>pdb|1PSY|A Chain A, Structure Of Ricc3, Nmr, 20 Structures
Length = 125
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 193 KSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANE 231
+ GS+S++ R VQ D S RYLR SSSR T E
Sbjct: 10 REGSSSQQCRQEVQRKDLSSCERYLR--QSSSRRSTGEE 46
>pdb|3I1J|A Chain A, Structure Of A Putative Short Chain Dehydrogenase From
Pseudomonas Syringae
pdb|3I1J|B Chain B, Structure Of A Putative Short Chain Dehydrogenase From
Pseudomonas Syringae
Length = 247
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 117 ASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRS 168
ASIIG +E P+E++ + +N +A T L LL+ SIA S
Sbjct: 102 ASIIGPRTPLEQLPDEDFXQVXHVNVNATFXLTRALLPLLKRSEDASIAFTS 153
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
0.312 0.126 0.344
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,901,735
Number of Sequences: 62578
Number of extensions: 208211
Number of successful extensions: 505
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 486
Number of HSP's gapped (non-prelim): 13
length of query: 328
length of database: 14,973,337
effective HSP length: 99
effective length of query: 229
effective length of database: 8,778,115
effective search space: 2010188335
effective search space used: 2010188335
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)