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= 006240
         (655 letters)

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

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



>pdb|2GWM|A Chain A, Crystal Structure Of The Salmonella Spvb Atr Domain
          Length = 200

 Score = 30.0 bits (66), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 381 SVVVGKAAIGNMLGGIGYFYGQSKVSLPKNTKLK 414
           ++ + K   G +LG + +F G++++  P NTKLK
Sbjct: 125 NIYLEKGHKGRILGDVAHFKGEAEMLFPPNTKLK 158


>pdb|2GWL|A Chain A, Crystal Structure Of The Salmonella Spvb Atr Domain In
           Complex With Nadh
          Length = 200

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 381 SVVVGKAAIGNMLGGIGYFYGQSKVSLPKNTKLK 414
           ++ + K   G +LG + +F G++++  P NTKLK
Sbjct: 124 NIYLEKGHKGRILGDVAHFKGEAEMLFPPNTKLK 157


  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    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,888,283
Number of Sequences: 62578
Number of extensions: 794511
Number of successful extensions: 1474
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1472
Number of HSP's gapped (non-prelim): 3
length of query: 655
length of database: 14,973,337
effective HSP length: 105
effective length of query: 550
effective length of database: 8,402,647
effective search space: 4621455850
effective search space used: 4621455850
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)