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= psy5720
         (153 letters)

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

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



>pdb|2W3E|A Chain A, Oxidized Structure Of The First Gaf Domain Of
           Mycobacterium Tuberculosis Doss
 pdb|2W3E|B Chain B, Oxidized Structure Of The First Gaf Domain Of
           Mycobacterium Tuberculosis Doss
 pdb|2W3F|A Chain A, Reduced Structure Of The First Gaf Domain Of Mycobacterium
           Tuberculosis Doss
 pdb|2W3F|B Chain B, Reduced Structure Of The First Gaf Domain Of Mycobacterium
           Tuberculosis Doss
 pdb|2W3G|A Chain A, Air-Oxidized Structure Of The First Gaf Domain Of
           Mycobacterium Tuberculosis Doss
 pdb|2W3G|B Chain B, Air-Oxidized Structure Of The First Gaf Domain Of
           Mycobacterium Tuberculosis Doss
 pdb|2W3H|A Chain A, Cyanide Bound Structure Of The First Gaf Domain Of
           Mycobacterium Tuberculosis Doss
 pdb|2W3H|B Chain B, Cyanide Bound Structure Of The First Gaf Domain Of
           Mycobacterium Tuberculosis Doss
          Length = 153

 Score = 27.7 bits (60), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 50  PKLEKRLRATMERVKALETALKEAKEGAMKDRKRYQYEVDRIKEAVRQKNLARRGPAPQ 108
           P LE  LRA +       T+L +A+ GAM+   R    +  + E + ++ + R G  P+
Sbjct: 5   PDLEATLRAIVHSA----TSLVDARYGAMEVHDRQHRVLHFVYEGIDEETVRRIGHLPK 59


  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
   0.314    0.131    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,781,015
Number of Sequences: 62578
Number of extensions: 118310
Number of successful extensions: 304
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 285
Number of HSP's gapped (non-prelim): 31
length of query: 153
length of database: 14,973,337
effective HSP length: 90
effective length of query: 63
effective length of database: 9,341,317
effective search space: 588502971
effective search space used: 588502971
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)