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= 008375
         (568 letters)

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

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



>pdb|4AQ4|A Chain A, Substrate Bound Sn-Glycerol-3-Phosphate Binding
           Periplasmic Protein Ugpb From Escherichia Coli
          Length = 419

 Score = 30.0 bits (66), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)

Query: 339 PAEPPLAWQDTNGYDA-MQAQALAGGYQGEWQDYQYAEQLA 378
           P +PP  WQD   Y A ++A  +  GY   WQ +   E  +
Sbjct: 143 PEQPPKTWQDLADYAAKLKASGMKCGYASGWQGWIQLENFS 183


  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
   0.311    0.131    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,246,500
Number of Sequences: 62578
Number of extensions: 708661
Number of successful extensions: 1051
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1051
Number of HSP's gapped (non-prelim): 4
length of query: 568
length of database: 14,973,337
effective HSP length: 104
effective length of query: 464
effective length of database: 8,465,225
effective search space: 3927864400
effective search space used: 3927864400
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)