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= 038954
         (69 letters)

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

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



>pdb|2YHB|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
           Domains
          Length = 437

 Score = 26.2 bits (56), Expect = 4.8,   Method: Composition-based stats.
 Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 4/38 (10%)

Query: 12  PTGPKTIHFWAPTFKWGISIANIADFSNYNMKNWNLFI 49
           PT PK IHF + + K G     + D    N++ W+ F+
Sbjct: 293 PTDPKHIHFKSKSPKEG----TVVDRGVTNVRYWDFFL 326


>pdb|3BU7|A Chain A, Crystal Structure And Biochemical Characterization Of
           Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter
           Pomeroyi
 pdb|3BU7|B Chain B, Crystal Structure And Biochemical Characterization Of
           Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter
           Pomeroyi
          Length = 394

 Score = 25.8 bits (55), Expect = 6.0,   Method: Composition-based stats.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 9   WNHPTGPKTIHFWAPTFKWGISIANIADFSNYN 41
           W+ P  P   + W PT++  ++ A  +D S Y+
Sbjct: 243 WDKPYSPLLKYSWEPTYEALLNYAKASDGSPYD 275


>pdb|3KLY|A Chain A, Pentameric Formate Channel
 pdb|3KLY|B Chain B, Pentameric Formate Channel
 pdb|3KLY|C Chain C, Pentameric Formate Channel
 pdb|3KLY|D Chain D, Pentameric Formate Channel
 pdb|3KLY|E Chain E, Pentameric Formate Channel
 pdb|3KLZ|A Chain A, Pentameric Formate Channel With Formate Bound
 pdb|3KLZ|B Chain B, Pentameric Formate Channel With Formate Bound
 pdb|3KLZ|C Chain C, Pentameric Formate Channel With Formate Bound
 pdb|3KLZ|D Chain D, Pentameric Formate Channel With Formate Bound
 pdb|3KLZ|E Chain E, Pentameric Formate Channel With Formate Bound
          Length = 280

 Score = 25.8 bits (55), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 3/34 (8%)

Query: 18  IHFWAPTFKWGISIANIADFSNYNMKNWNLFIVN 51
           I ++AP   W ++ ANIA +++ N  N   FIVN
Sbjct: 222 IKYFAPESFWAMTGANIAQYADLNFVN---FIVN 252


  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
   0.325    0.136    0.463 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,032,451
Number of Sequences: 62578
Number of extensions: 59844
Number of successful extensions: 126
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 124
Number of HSP's gapped (non-prelim): 3
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)