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= 025279
         (255 letters)

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

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



>pdb|1NOX|A Chain A, Nadh Oxidase From Thermus Thermophilus
          Length = 205

 Score = 30.4 bits (67), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 140 RNPSAWKLQPGIQRTAVIYAAIVGTVIRSSIIAWCLQKKGPVFVALFKPLGTAIAVFMAV 199
           R PSAW LQP   R  V+        +R +       ++ PV + L+  L  A+A    V
Sbjct: 42  RAPSAWNLQPW--RIVVVRDPATKRALREAAFGQAHVEEAPVVLVLYADLEDALAHLDEV 99

Query: 200 MFLG 203
           +  G
Sbjct: 100 IHPG 103


>pdb|1W8X|P Chain P, Structural Analysis Of Prd1
          Length = 117

 Score = 27.3 bits (59), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 10/31 (32%), Positives = 20/31 (64%)

Query: 53 AFIVSLYKGPPLLGFSSPSNSNIQLPVSEYS 83
          A + S ++GPP + ++ P   ++ LPV+ Y+
Sbjct: 29 AQVASNWEGPPYMTYNQPQAGSVTLPVAGYT 59


  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
   0.324    0.137    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,076,309
Number of Sequences: 62578
Number of extensions: 261476
Number of successful extensions: 737
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: 735
Number of HSP's gapped (non-prelim): 3
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
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: 50 (23.9 bits)