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= psy13979
         (78 letters)

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

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



>pdb|1IK6|A Chain A, 3d Structure Of The E1beta Subunit Of Pyruvate
           Dehydrogenase From The Archeon Pyrobaculum Aerophilum
          Length = 369

 Score = 25.4 bits (54), Expect = 8.9,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 7/64 (10%)

Query: 21  GFMIGFSVGMATGGL--FGGFNALRYGLRGA-ELLKNVGKVMVQGGGSFGTFMA----IG 73
           G ++GF++GMA  GL        + +   GA ELL ++ K+  + GG++   +     +G
Sbjct: 108 GGILGFAMGMAMAGLKPVAEIQFVDFIWLGADELLNHIAKLRYRSGGNYKAPLVVRTPVG 167

Query: 74  AGIR 77
           +G R
Sbjct: 168 SGTR 171


  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
   0.328    0.148    0.464 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,434,088
Number of Sequences: 62578
Number of extensions: 92076
Number of successful extensions: 254
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 253
Number of HSP's gapped (non-prelim): 6
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)