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= 004487
         (749 letters)

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

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



>pdb|3ONQ|A Chain A, Crystal Structure Of Regulator Of Polyketide Synthase
           Expression Bad_0249 From Bifidobacterium Adolescentis
 pdb|3ONQ|B Chain B, Crystal Structure Of Regulator Of Polyketide Synthase
           Expression Bad_0249 From Bifidobacterium Adolescentis
 pdb|3ONQ|C Chain C, Crystal Structure Of Regulator Of Polyketide Synthase
           Expression Bad_0249 From Bifidobacterium Adolescentis
 pdb|3ONQ|D Chain D, Crystal Structure Of Regulator Of Polyketide Synthase
           Expression Bad_0249 From Bifidobacterium Adolescentis
          Length = 262

 Score = 30.8 bits (68), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 5/57 (8%)

Query: 47  YSQKNQFREAFKLFVDMRTDGGSDPDYVTFATLLS-GCSEPDTANELIQVHADIIKF 102
           Y+++  +R  +++   +R +   DP Y+T +T L  G S  +TA EL  VH + +++
Sbjct: 176 YAREELYRNVYQV---LRGENPDDPTYLTVSTFLKYGSSLENTAKEL-NVHPNTVRY 228


>pdb|1RD5|A Chain A, Crystal Structure Of Tryptophan Synthase Alpha Chain
           Homolog Bx1: A Member Of The Chemical Plant Defense
           System
 pdb|1RD5|B Chain B, Crystal Structure Of Tryptophan Synthase Alpha Chain
           Homolog Bx1: A Member Of The Chemical Plant Defense
           System
          Length = 262

 Score = 29.6 bits (65), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 582 PYVAMSNIYAVA--GQWESVSQVKKAMRERGVRKVTAYSWVELKSKVHVFTANDELHPQT 639
           PYVA  ++++ A     E V     A+ E  ++++T  S    +  V++ + N    P+ 
Sbjct: 128 PYVAAHSLWSEAKNNNLELVLLTTPAIPEDRMKEITKAS----EGFVYLVSVNGVTGPRA 183

Query: 640 NEIRRKIENLMQEMKKEGYKP 660
           N +  ++E+L+QE+KK   KP
Sbjct: 184 N-VNPRVESLIQEVKKVTNKP 203


  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
   0.321    0.133    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,031,712
Number of Sequences: 62578
Number of extensions: 768560
Number of successful extensions: 2056
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2055
Number of HSP's gapped (non-prelim): 9
length of query: 749
length of database: 14,973,337
effective HSP length: 106
effective length of query: 643
effective length of database: 8,340,069
effective search space: 5362664367
effective search space used: 5362664367
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)