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= psy14509
         (243 letters)

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

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



>pdb|1D1R|A Chain A, Nmr Solution Structure Of The Product Of The E. Coli Ycih
           Gene
          Length = 116

 Score = 29.6 bits (65), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 139 VCVSRAPRGKK-KSVTVVTGLSSFDIDLKVASKFFGTRFACGSSVTGDDEIVIQGDVKDD 197
           V + R   G+K K V ++TG+   D +L   +     +  CG +V  D  I IQGD +D 
Sbjct: 33  VRIQRQTSGRKGKGVCLITGVDLDDAELTKLAAELKKKCGCGGAVK-DGVIEIQGDKRDL 91

Query: 198 LFDVIPEKWPEI 209
           L  ++  K  ++
Sbjct: 92  LKSLLEAKGMKV 103


  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
   0.316    0.138    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,896,312
Number of Sequences: 62578
Number of extensions: 344744
Number of successful extensions: 566
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 564
Number of HSP's gapped (non-prelim): 4
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)