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= psy17939
         (81 letters)

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

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



>pdb|2O1X|A Chain A, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
 pdb|2O1X|B Chain B, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
 pdb|2O1X|C Chain C, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
 pdb|2O1X|D Chain D, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
          Length = 629

 Score = 28.1 bits (61), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 27/48 (56%)

Query: 9   IEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKL 56
           ++ GD  + +   K +   +   E LPG+ ++  RFV P+ + M++++
Sbjct: 502 LKGGDDVVILAGGKALDYALKAAEDLPGVGVVNARFVKPLDEEMLREV 549


>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
           PolymerasePCNA Monomer Mutant Complex
          Length = 775

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 24/43 (55%)

Query: 9   IEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDH 51
           ++ GD +  +  +K+VIQ +AN E  P  L I  +   P+ ++
Sbjct: 632 LKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEY 674


>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
          Length = 775

 Score = 25.8 bits (55), Expect = 6.6,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 24/43 (55%)

Query: 9   IEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDH 51
           ++ GD +  +  +K+VIQ +AN E  P  L I  +   P+ ++
Sbjct: 632 LKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEY 674


>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
 pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
 pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
          Length = 775

 Score = 25.8 bits (55), Expect = 6.7,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 24/43 (55%)

Query: 9   IEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDH 51
           ++ GD +  +  +K+VIQ +AN E  P  L I  +   P+ ++
Sbjct: 632 LKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEY 674


  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
   0.327    0.143    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,449,175
Number of Sequences: 62578
Number of extensions: 72009
Number of successful extensions: 182
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 178
Number of HSP's gapped (non-prelim): 4
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)