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= 023941
         (275 letters)

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

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



>pdb|2F5U|A Chain A, Structural Characterization Of The Ul25 Dna Packaging
           Protein From Herpes Simplex Virus Type 1
          Length = 447

 Score = 29.6 bits (65), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 4/38 (10%)

Query: 10  AIKSYQNQAQVLVKNYII----ADPFIPYTSILAGLLA 43
           AIKS  N  + L  NY++    ADP +  T +  GL A
Sbjct: 299 AIKSGDNNLEALCANYVLPLYRADPAVELTQLFPGLAA 336


>pdb|1FFT|A Chain A, The Structure Of Ubiquinol Oxidase From Escherichia Coli
 pdb|1FFT|F Chain F, The Structure Of Ubiquinol Oxidase From Escherichia Coli
          Length = 663

 Score = 28.5 bits (62), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 18/29 (62%)

Query: 230 HYDQVVEMHAIGYLLVFVVPFVLAIMNVM 258
           HYDQ+   H +  +    +PFV+ +MN++
Sbjct: 98  HYDQIFTAHGVIMIFFVAMPFVIGLMNLV 126


  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
   0.329    0.140    0.436 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,900,549
Number of Sequences: 62578
Number of extensions: 315597
Number of successful extensions: 783
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 782
Number of HSP's gapped (non-prelim): 18
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)