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= 044308
         (645 letters)

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

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



>pdb|3AAM|A Chain A, Crystal Structure Of Endonuclease Iv From Thermus
           Thermophilus Hb8
          Length = 270

 Score = 29.3 bits (64), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 11/80 (13%)

Query: 21  REWFPPTRALAALSAFRQTREVFAATKRLNPNPQHQSP-ANISADSESALESIASLGDDP 79
           R W P   + A + AFR  RE         P   H S   N+ A+ E   +S+ASL DD 
Sbjct: 39  RSWRPRALSPAEVEAFRALREASGGL----PAVIHASYLVNLGAEGELWEKSVASLADDL 94

Query: 80  LAASSGQLIVGVESRYRVVY 99
             A+    ++GVE  Y VV+
Sbjct: 95  EKAA----LLGVE--YVVVH 108


  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
   0.315    0.131    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,656,568
Number of Sequences: 62578
Number of extensions: 618482
Number of successful extensions: 1301
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1300
Number of HSP's gapped (non-prelim): 4
length of query: 645
length of database: 14,973,337
effective HSP length: 105
effective length of query: 540
effective length of database: 8,402,647
effective search space: 4537429380
effective search space used: 4537429380
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)