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= 028279
         (211 letters)

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

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



>pdb|1RI6|A Chain A, Structure Of A Putative Isomerase From E. Coli
          Length = 343

 Score = 29.6 bits (65), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 5/99 (5%)

Query: 98  ASFKHGSGKSLLLYRGKQVGVVDIDPGLIPARGSAVLPSRLTLQVDEVASNLSALIRDVL 157
            S+  G+     L  G  VGVVD+  GL     + + P   TL V  +  +   L     
Sbjct: 101 GSYNAGNVSVTRLEDGLPVGVVDVVEGLDGCHSANISPDNRTLWVPALKQDRICLFTVSD 160

Query: 158 DGELVMETHTRIPGRVNLL-GIFKKHIVATSECQFTFSV 195
           DG LV +     P  V  + G   +H+V     Q+ + V
Sbjct: 161 DGHLVAQD----PAEVTTVEGAGPRHMVFHPNEQYAYCV 195


  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    0.137    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,536,120
Number of Sequences: 62578
Number of extensions: 153138
Number of successful extensions: 342
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: 340
Number of HSP's gapped (non-prelim): 2
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
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)