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= 030838
         (170 letters)

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

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



>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
 pdb|1A77|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
          Length = 326

 Score = 29.3 bits (64), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 127 MKEAVAEERFEDAARYRDKLKEIAPNSLLKC 157
           MKEA+ +E FE+AA+Y  ++  + P  +  C
Sbjct: 105 MKEAIKKEDFEEAAKYAKRVSYLTPKMVENC 135


>pdb|3Q0I|A Chain A, Methionyl-Trna Formyltransferase From Vibrio Cholerae
          Length = 318

 Score = 28.9 bits (63), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 134 ERFEDAARYRDKLKEIAPNSLLKCLSD 160
           E  + +A   DKL E+ P +LL+CL D
Sbjct: 163 EASDTSASXYDKLAELGPQALLECLQD 189


  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
   0.321    0.133    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,612,861
Number of Sequences: 62578
Number of extensions: 104052
Number of successful extensions: 328
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 319
Number of HSP's gapped (non-prelim): 9
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)