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= 012492
         (462 letters)

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

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



>pdb|3S2U|A Chain A, Crystal Structure Of The Pseudomonas Aeruginosa
           Murg:udp-Glcnac Substrate Complex
          Length = 365

 Score = 36.2 bits (82), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 8/115 (6%)

Query: 334 FETQMEKWMGACDCIITKAGPGTIAEALIRGLP---IILNDYIPGQEKGNVPYVVDNGAG 390
           F + M       D +I +AG  T++E    GLP   + L   I   +  N  ++V +GAG
Sbjct: 242 FISDMAAAYAWADLVICRAGALTVSELTAAGLPAFLVPLPHAIDDHQTRNAEFLVRSGAG 301

Query: 391 VF----TRSPKETARIVTEWFSTKTDELKRMSENALKLAQPEAVVDIVKDIHDLA 441
                 +    E A  ++E      + L+ M++ A  LA+PEA   +V    ++A
Sbjct: 302 RLLPQKSTGAAELAAQLSEVL-MHPETLRSMADQARSLAKPEATRTVVDACLEVA 355


  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    0.136    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,779,291
Number of Sequences: 62578
Number of extensions: 510559
Number of successful extensions: 1125
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1122
Number of HSP's gapped (non-prelim): 5
length of query: 462
length of database: 14,973,337
effective HSP length: 102
effective length of query: 360
effective length of database: 8,590,381
effective search space: 3092537160
effective search space used: 3092537160
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: 53 (25.0 bits)