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= 001257
         (1113 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 = 3.1,   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 = 29.6 bits (65), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 7/60 (11%)

Query: 851 ADEIRQEAYKHWQSLKKQAYDKNQHFWKYKDDTKQANDLASKGDREALQHLCVNQVERVL 910
           +DE ++  YK+W   KK+A+ K    W+  D  KQ        D  +++  C  QV RV+
Sbjct: 111 SDECKRRFYKNWHKSKKKAFTKYCKKWQDADGKKQLER-----DFSSMKKYC--QVIRVI 163


>pdb|3IXQ|A Chain A, Structure Of Ribose 5-Phosphate Isomerase A From
           Methanocaldococcus Jannaschii
 pdb|3IXQ|B Chain B, Structure Of Ribose 5-Phosphate Isomerase A From
           Methanocaldococcus Jannaschii
 pdb|3IXQ|C Chain C, Structure Of Ribose 5-Phosphate Isomerase A From
           Methanocaldococcus Jannaschii
 pdb|3IXQ|D Chain D, Structure Of Ribose 5-Phosphate Isomerase A From
           Methanocaldococcus Jannaschii
          Length = 226

 Score = 29.6 bits (65), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 33/115 (28%), Positives = 53/115 (46%), Gaps = 7/115 (6%)

Query: 748 IRNMEHRIAHETLPLKEEKQIIREIKQLKQRREQISSSIGEHDEVQLAFDQKDQIEEKMK 807
           IR + +RI  E L +        E K L  + E    ++ E+D V +AFD  D++EE   
Sbjct: 36  IRELGNRIREEELTVFGIPTSF-EAKMLAMQYEIPLVTLDEYD-VDIAFDGADEVEETTL 93

Query: 808 FLRKEADSL--RENVIKAEAATQAVKKLHREESEKLKRLLGQFKAADEIRQEAYK 860
           FL K       +E ++   A    V     +ES+ +K+L  +F    E+   AY+
Sbjct: 94  FLIKGGGGCHTQEKIVDYNANEFVV---LVDESKLVKKLGEKFPIPVEVIPSAYR 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    0.344 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,640,952
Number of Sequences: 62578
Number of extensions: 1154476
Number of successful extensions: 2650
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 2611
Number of HSP's gapped (non-prelim): 65
length of query: 1113
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1004
effective length of database: 8,152,335
effective search space: 8184944340
effective search space used: 8184944340
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)