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= 005115
         (714 letters)

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

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



>pdb|3IRA|A Chain A, The Crystal Structure Of One Domain Of The Conserved
           Protein From Methanosarcina Mazei Go1
          Length = 173

 Score =  114 bits (286), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 71/104 (68%)

Query: 21  CHVMEVESFEDEGVAKLLNDWFVSIKVDREERPDVDKVYMTYVQALYGGGGWPLSVFLSP 80
           CH+M  ESFEDE VA L+N+ FVSIKVDREERPD+D +YMT  Q + G GGWPL++ ++P
Sbjct: 54  CHMMAHESFEDEEVAGLMNEAFVSIKVDREERPDIDNIYMTVCQIILGRGGWPLNIIMTP 113

Query: 81  DLKPLMGGTYFPPEDKYGRPGFKTILRKVKDAWDKKRDMLAQSG 124
             KP   GTY P   ++ + G   ++ ++K+ W+++ + +  S 
Sbjct: 114 GKKPFFAGTYIPKNTRFNQIGMLELVPRIKEIWEQQHEEVLDSA 157


>pdb|1D02|A Chain A, Crystal Structure Of Muni Restriction Endonuclease In
           Complex With Cognate Dna
 pdb|1D02|B Chain B, Crystal Structure Of Muni Restriction Endonuclease In
           Complex With Cognate Dna
          Length = 202

 Score = 30.0 bits (66), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 14/35 (40%), Positives = 19/35 (54%)

Query: 649 IHIDPADTEEMDFWEEHNSNNASMARNNFSADKVV 683
           I  DP    E+ FW +H  +N  M R N S +K+V
Sbjct: 156 ITRDPKRVREITFWYDHYQDNYFMWRPNESGEKLV 190


  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
   0.318    0.135    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,333,838
Number of Sequences: 62578
Number of extensions: 989981
Number of successful extensions: 1954
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1950
Number of HSP's gapped (non-prelim): 7
length of query: 714
length of database: 14,973,337
effective HSP length: 106
effective length of query: 608
effective length of database: 8,340,069
effective search space: 5070761952
effective search space used: 5070761952
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)