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= 010658
         (505 letters)

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

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



>pdb|1IMU|A Chain A, Solution Structure Of Hi0257, A Ribosome Binding Protein
          Length = 107

 Score = 28.9 bits (63), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 29 KWKAQSIS--IVILHVTYNISIKDFVYTPFGKLPATSLSDEKLEILKKYEQ 77
          KW+ Q IS   V+  V    S++  + TP G L A++ SD+  + + + E+
Sbjct: 29 KWQTQLISPHFVLNKVPNGFSVEASIGTPLGNLLASATSDDMYKAINEVEE 79


  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
   0.317    0.132    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,091,523
Number of Sequences: 62578
Number of extensions: 556341
Number of successful extensions: 1431
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1427
Number of HSP's gapped (non-prelim): 7
length of query: 505
length of database: 14,973,337
effective HSP length: 103
effective length of query: 402
effective length of database: 8,527,803
effective search space: 3428176806
effective search space used: 3428176806
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)