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= 025164
         (257 letters)

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

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



>pdb|2YWR|A Chain A, Crystal Structure Of Gar Transformylase From Aquifex
           Aeolicus
          Length = 216

 Score = 30.4 bits (67), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 4/42 (9%)

Query: 104 DFCSRPILDIRGKKIWELVVCDG---SLSLQYTKYFPNNVIN 142
           +F  R  L+++ K + ELVV  G    LS  + KYFPN VIN
Sbjct: 67  EFEERXALELKKKGV-ELVVLAGFXRILSHNFLKYFPNKVIN 107


>pdb|1LRZ|A Chain A, X-Ray Crystal Structure Of Staphylococcus Aureus Fema
          Length = 426

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 26/138 (18%), Positives = 49/138 (35%), Gaps = 29/138 (21%)

Query: 126 GSLSLQYTKYFPNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKACKELDI 185
           G   L+  + +  +++        ++A C    VP+ +  ++F S    +I    +EL  
Sbjct: 28  GHYELKLAEGYETHLVGIKNNNNEVIAACLLTAVPVMKVFKYFYSNRGPVIDYENQELVH 87

Query: 186 -------KPIPSKRCLSLLL----------------------WLEERYETVYTRHPGFQK 216
                  K +   RCL L +                      W  ++   +   H GF K
Sbjct: 88  FFFNELSKYVKKHRCLYLHIDPYLPYQYLNHDGEITGNAGNDWFFDKMSNLGFEHTGFHK 147

Query: 217 GSKPLLALDNPFPMELPD 234
           G  P+L +     ++L D
Sbjct: 148 GFDPVLQIRYHSVLDLKD 165


  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
   0.320    0.138    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,245,953
Number of Sequences: 62578
Number of extensions: 283372
Number of successful extensions: 527
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 526
Number of HSP's gapped (non-prelim): 2
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)