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= psy16397
         (60 letters)

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

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



>pdb|1MZU|A Chain A, Crystal Structure Of The Photoactive Yellow Protein Domain
           From The Sensor Histidine Kinase Ppr From Rhodospirillum
           Centenum
 pdb|1MZU|B Chain B, Crystal Structure Of The Photoactive Yellow Protein Domain
           From The Sensor Histidine Kinase Ppr From Rhodospirillum
           Centenum
 pdb|1MZU|C Chain C, Crystal Structure Of The Photoactive Yellow Protein Domain
           From The Sensor Histidine Kinase Ppr From Rhodospirillum
           Centenum
          Length = 129

 Score = 26.9 bits (58), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 7/44 (15%)

Query: 7   GLTEGTLTAMLDFYIDNEM------IHIADTKVAHRYGDFFIRK 44
           G+T GTL A  DF  D +M      I + +  V  RY   F+RK
Sbjct: 87  GVTSGTLDARFDFVFDFQMAPVRVQIRMQNAGVPDRYW-IFVRK 129


  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
   0.326    0.142    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,566,679
Number of Sequences: 62578
Number of extensions: 47110
Number of successful extensions: 261
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 261
Number of HSP's gapped (non-prelim): 1
length of query: 60
length of database: 14,973,337
effective HSP length: 31
effective length of query: 29
effective length of database: 13,033,419
effective search space: 377969151
effective search space used: 377969151
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)