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= 019233
(344 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 31.2 bits (69), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 79 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 128
Query: 318 LGIPFSDLLQVSRHAL 333
G+ F DL+Q L
Sbjct: 129 RGLSFLDLIQEGNQGL 144
>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 = 31.2 bits (69), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 83 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132
Query: 318 LGIPFSDLLQVSRHAL 333
G+ F DL+Q L
Sbjct: 133 RGLSFLDLIQEGNQGL 148
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 170 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 219
Query: 318 LGIPFSDLLQVSRHAL 333
G+ F DL+Q L
Sbjct: 220 RGLSFLDLIQEGNQGL 235
>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 = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 286 LKQHLAF---GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHAL 333
LK++L G R+ LI++ LV+ +A+ Y G G+ F DL+Q L
Sbjct: 79 LKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGL 129
>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 = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 261 TLEKESGKAASLNCWAQAAGVSERVLKQHLAF---GWYCREELIKSTRPLVLFLARNYRG 317
T+E+ GK SL + LK++L G R+ LI++ LV+ +A+ Y G
Sbjct: 78 TVEEVDGKLKSLP----------KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 127
Query: 318 LGIPFSDLLQVSRHAL 333
G+ F DL+Q L
Sbjct: 128 RGLSFLDLIQEGNQGL 143
>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 = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHAL 333
H+A G R+ LI++ LV+ +A+ Y G G+ F DL+Q L
Sbjct: 195 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGL 240
>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 = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHAL 333
H+A G R+ LI++ LV+ +A+ Y G G+ F DL+Q L
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGL 220
>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 = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 289 HLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHAL 333
H+A G R+ LI++ LV+ +A+ Y G G+ F DL+Q L
Sbjct: 175 HIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGL 220
>pdb|1YY5|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1YY5|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|A Chain A, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|B Chain B, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|C Chain C, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
pdb|1XPQ|D Chain D, Crystal Structure Of Fms1, A Polyamine Oxidase From Yeast
Length = 513
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQA 278
N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 308 NESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQP 357
>pdb|1VDK|A Chain A, Crystal Structure Of Fumarase From Thermus Thermophilus
Hb8
pdb|1VDK|B Chain B, Crystal Structure Of Fumarase From Thermus Thermophilus
Hb8
Length = 466
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 14/90 (15%)
Query: 238 IARNEAEMSKGVQVVANLERIKTTLEKESGKAASLN---CWAQAAGVSERVLKQH----- 289
+A +A +++G++ NLERI+ L+K A +LN + +AA + ++ LK+
Sbjct: 380 VASFDAHLAQGIE--PNLERIEEYLQKNPMLATALNKAIGYDKAAEIVKKALKEKKTLKQ 437
Query: 290 --LAFGWYCREELIKSTRPLVLFLARNYRG 317
L G+ EE + P + LA+ + G
Sbjct: 438 AALELGYLTEEEFDRIVVP--MRLAKPHEG 465
>pdb|1Z6L|A Chain A, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|1Z6L|B Chain B, Crystal Structure Of Fms1 In Complex With Its Substrate
pdb|3BI2|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI2|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI4|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|A Chain A, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BI5|B Chain B, Crystal Structures Of Fms1 In Complex With Its Inhibitors
pdb|3BNM|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNM|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3r,3'r)-
Methylated Spermine
pdb|3BNU|B Chain B, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3BNU|A Chain A, Crystal Structure Of Polyamine Oxidase Fms1 From
Saccharomyces Cerevisiae In Complex With Bis-(3s,3's)-
Methylated Spermine
pdb|3CN8|B Chain B, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CN8|A Chain A, Crystal Structure Of Fms1 In Complex With Spermidine
pdb|3CND|B Chain B, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CND|A Chain A, Crystal Structure Of Fms1 In Complex With N1-Acspermine
pdb|3CNP|B Chain B, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNP|A Chain A, Crystal Structure Of Fms1 In Complex With
S-n1-acmespermidine
pdb|3CNS|A Chain A, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNS|B Chain B, Crystal Structure Of Fms1 In Complex With
S-Bz-Mespermidine
pdb|3CNT|B Chain B, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
pdb|3CNT|A Chain A, Crystal Structure Of Fms1 In Complex With
R-Bz-Mespermidine
Length = 516
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQA 278
N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 308 NESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQP 357
>pdb|4GDP|A Chain A, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|B Chain B, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|C Chain C, Yeast Polyamine Oxidase Fms1, N195a Mutant
pdb|4GDP|D Chain D, Yeast Polyamine Oxidase Fms1, N195a Mutant
Length = 516
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQA 278
N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 308 NESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQP 357
>pdb|1RSG|A Chain A, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
pdb|1RSG|B Chain B, Crystal Structure Of The Polyamine Oxidase Fms1 From Yeast
Length = 516
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQA 278
N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 308 NESSKIVTLANSTNEFVEIVRNAENLDELDSXLEREDSQKHTSVTCWSQP 357
>pdb|4ECH|A Chain A, Yeast Polyamine Oxidase Fms1, H67q Mutant
pdb|4ECH|B Chain B, Yeast Polyamine Oxidase Fms1, H67q Mutant
Length = 516
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKE-SGKAASLNCWAQA 278
N + +T+A + E + V+ NL+ + + LE+E S K S+ CW+Q
Sbjct: 308 NESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQP 357
>pdb|4GIC|A Chain A, Crystal Structure Of A Putative Histidinol Dehydrogenase
(Target Psi- 014034) From Methylococcus Capsulatus
pdb|4GIC|B Chain B, Crystal Structure Of A Putative Histidinol Dehydrogenase
(Target Psi- 014034) From Methylococcus Capsulatus
Length = 423
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 256 ERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTR 305
E I+T+LE+ G ++ QAA V+ R+ +HL E L++S R
Sbjct: 302 EVIRTSLERRGGXIL-VDDLEQAAAVANRIAPEHLELSVESPEVLVESIR 350
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
0.318 0.130 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,909,195
Number of Sequences: 62578
Number of extensions: 258888
Number of successful extensions: 766
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 758
Number of HSP's gapped (non-prelim): 17
length of query: 344
length of database: 14,973,337
effective HSP length: 100
effective length of query: 244
effective length of database: 8,715,537
effective search space: 2126591028
effective search space used: 2126591028
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)