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= psy3244
         (569 letters)

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

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



>pdb|2BGW|A Chain A, Xpf From Aeropyrum Pernix, Complex With Dna
 pdb|2BGW|B Chain B, Xpf From Aeropyrum Pernix, Complex With Dna
          Length = 219

 Score = 30.8 bits (68), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 8/83 (9%)

Query: 206 GSRPLLSFDEKFSQEPHYRLMQELLTQIFGTPKDLPKSQPFIDHVISFSILDNRIWFRNY 265
           G RP +  D +  + P   +++ L  Q+      +PK  P  D+++S SI+  R    ++
Sbjct: 6   GGRPRVYVDVREERSPVPSILESLGVQV------IPKQLPMGDYLVSDSIIVERKTSSDF 59

Query: 266 QILSEDGALFRQQLKRLAGQKYE 288
                DG LF +Q  RLA + YE
Sbjct: 60  AKSLFDGRLF-EQASRLA-EHYE 80


  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
   0.317    0.134    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,459,646
Number of Sequences: 62578
Number of extensions: 491981
Number of successful extensions: 1031
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1016
Number of HSP's gapped (non-prelim): 20
length of query: 569
length of database: 14,973,337
effective HSP length: 104
effective length of query: 465
effective length of database: 8,465,225
effective search space: 3936329625
effective search space used: 3936329625
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: 54 (25.4 bits)