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= 000924
         (1222 letters)

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

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



>pdb|1B8P|A Chain A, Malate Dehydrogenase From Aquaspirillum Arcticum
 pdb|1B8U|A Chain A, Malate Dehydrogenase From Aquaspirillum Arcticum
 pdb|1B8V|A Chain A, Malate Dehydrogenase From Aquaspirillum Arcticum
          Length = 329

 Score = 31.2 bits (69), Expect = 3.4,   Method: Composition-based stats.
 Identities = 18/38 (47%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 615 GIERSDRCET--QTSTPEGSTVDASESRNIGVEVVKQP 650
           G+ER D  E   Q  T +G  +DA  SRNI V VV  P
Sbjct: 98  GMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNP 135


>pdb|2ZKR|BB Chain b, Structure Of A Mammalian Ribosomal 60s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 403

 Score = 30.8 bits (68), Expect = 5.3,   Method: Composition-based stats.
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 851 ADEIRQEAYKHWQSLKKQAYDKNQHFWKYKDDTKQ 885
           +DE ++  YK+W   KK+A+ K    W+  D  KQ
Sbjct: 111 SDECKRRFYKNWHKSKKKAFTKYCKKWQDADGKKQ 145


  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
   0.308    0.127    0.348 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,887,369
Number of Sequences: 62578
Number of extensions: 1183136
Number of successful extensions: 2666
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 2630
Number of HSP's gapped (non-prelim): 53
length of query: 1222
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1112
effective length of database: 8,089,757
effective search space: 8995809784
effective search space used: 8995809784
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 57 (26.6 bits)