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= 028854
         (202 letters)

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

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



>pdb|3LFT|A Chain A, The Crystal Structure Of The Abc Domain In Complex With
           L-Trp From Streptococcus Pneumonia To 1.35a
 pdb|3LFT|B Chain B, The Crystal Structure Of The Abc Domain In Complex With
           L-Trp From Streptococcus Pneumonia To 1.35a
          Length = 295

 Score = 28.9 bits (63), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 25  RDGVEFHVDKIPGTNQVKARGTVYLSNIRVVFVASKPVGNFVAFDMPLLYIHDEKFNQPI 84
           + G+      +P TN++ +  TV  S +  ++V   P+ N +A   P +   ++   +PI
Sbjct: 160 KAGLTVETFAVPSTNEIASTVTVXTSKVDAIWV---PIDNTIASGFPTVVSSNQSSKKPI 216

Query: 85  F 85
           +
Sbjct: 217 Y 217


  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
   0.322    0.138    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,204,589
Number of Sequences: 62578
Number of extensions: 245959
Number of successful extensions: 382
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 382
Number of HSP's gapped (non-prelim): 1
length of query: 202
length of database: 14,973,337
effective HSP length: 94
effective length of query: 108
effective length of database: 9,091,005
effective search space: 981828540
effective search space used: 981828540
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: 49 (23.5 bits)