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= psy15689
         (295 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
 pdb|1I6V|B Chain B, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 314

 Score = 30.4 bits (67), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 10/92 (10%)

Query: 47  DYIMEPGIFSQLKRYFQAG-GNPEQVIELLSQNYKAVAQ--MANLVAEWLILGGVNVTEV 103
           ++++EP     L+R F    GNP + I L S    AV    + +++ E+  + GV    V
Sbjct: 22  EFVLEP-----LERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVV 76

Query: 104 QAMVENHLKDMILKTFDPKKADTIFTEEGETP 135
           + ++  +LK+++++  DPK A T      E P
Sbjct: 77  EIIL--NLKELVVRFLDPKMASTTLILRAEGP 106


>pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|B Chain B, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|J Chain J, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9U|K Chain K, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 pdb|1L9Z|A Chain A, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 pdb|1L9Z|B Chain B, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 pdb|1YNJ|A Chain A, Taq Rna Polymerase-Sorangicin Complex
 pdb|1YNJ|B Chain B, Taq Rna Polymerase-Sorangicin Complex
 pdb|1YNN|A Chain A, Taq Rna Polymerase-rifampicin Complex
 pdb|1YNN|B Chain B, Taq Rna Polymerase-rifampicin Complex
 pdb|2GHO|A Chain A, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
 pdb|2GHO|B Chain B, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
          Length = 314

 Score = 30.4 bits (67), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 47/92 (51%), Gaps = 10/92 (10%)

Query: 47  DYIMEPGIFSQLKRYFQAG-GNPEQVIELLSQNYKAVAQ--MANLVAEWLILGGVNVTEV 103
           ++++EP     L+R F    GNP + I L S    AV    + +++ E+  + GV    V
Sbjct: 22  EFVLEP-----LERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVV 76

Query: 104 QAMVENHLKDMILKTFDPKKADTIFTEEGETP 135
           + ++  +LK+++++  DPK A T      E P
Sbjct: 77  EIIL--NLKELVVRFLDPKMASTTLILRAEGP 106


  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    0.130    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,532,066
Number of Sequences: 62578
Number of extensions: 254280
Number of successful extensions: 623
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 623
Number of HSP's gapped (non-prelim): 2
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
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)