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= 010062
         (519 letters)

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

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



>pdb|4GF4|A Chain A, Low Ph Structure Of Pseudomonas Putida Oprb
          Length = 436

 Score = 29.6 bits (65), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 19/36 (52%), Gaps = 3/36 (8%)

Query: 245 WGGCMMMHAD---DFRLDRYGVVSGLRDGGYSDDMT 277
           WGG      D   DF LD  G V+G   GGY+DD T
Sbjct: 30  WGGTRTELLDKGYDFTLDYVGEVAGNLHGGYNDDKT 65


>pdb|4GEY|A Chain A, High Ph Structure Of Pseudomonas Putida Oprb
          Length = 436

 Score = 29.6 bits (65), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 19/36 (52%), Gaps = 3/36 (8%)

Query: 245 WGGCMMMHAD---DFRLDRYGVVSGLRDGGYSDDMT 277
           WGG      D   DF LD  G V+G   GGY+DD T
Sbjct: 30  WGGTRTELLDKGYDFTLDYVGEVAGNLHGGYNDDKT 65


  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
   0.325    0.139    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,280,282
Number of Sequences: 62578
Number of extensions: 621933
Number of successful extensions: 1200
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1198
Number of HSP's gapped (non-prelim): 2
length of query: 519
length of database: 14,973,337
effective HSP length: 103
effective length of query: 416
effective length of database: 8,527,803
effective search space: 3547566048
effective search space used: 3547566048
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)