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= 036031
         (541 letters)

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

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



>pdb|2NYA|A Chain A, Crystal Structure Of The Periplasmic Nitrate Reductase
           (Nap) From Escherichia Coli
 pdb|2NYA|F Chain F, Crystal Structure Of The Periplasmic Nitrate Reductase
           (Nap) From Escherichia Coli
          Length = 792

 Score = 33.5 bits (75), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 64/153 (41%), Gaps = 10/153 (6%)

Query: 174 WQDSSNFSDVFDEDHFINSLANDVKVIKKVPKELSTA-ARAVKHFRSWSGMDYYEGEIAS 232
           W+D  NF  V D    +++LA D+ +   +  E   A   A +  + W       GE  S
Sbjct: 462 WRDPRNFIIVSDPYPTVSALAADLILPTAMWVEKEGAYGNAERRTQFWRQQVQAPGEAKS 521

Query: 233 -MWEDYQIIRAAKSDSRLANNNLPLDIQKLRCRACYEALRFAPQI------EAMGKLLVD 285
            +W+  Q  R  K++  +   +L     +LR +  YE L   P++      E     L D
Sbjct: 522 DLWQLVQFSRRFKTEE-VWPEDLLAKKPELRGKTLYEVLYATPEVSKFPVSELAEDQLND 580

Query: 286 RMRSYGPYIALHLRYEKDMLAFSGCTHDLSPVE 318
             R  G Y+   L +E+      G  HDL+P +
Sbjct: 581 ESRELGFYLQKGL-FEEYAWFGRGHGHDLAPFD 612


  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
   0.319    0.134    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,579,122
Number of Sequences: 62578
Number of extensions: 653473
Number of successful extensions: 1353
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1345
Number of HSP's gapped (non-prelim): 10
length of query: 541
length of database: 14,973,337
effective HSP length: 104
effective length of query: 437
effective length of database: 8,465,225
effective search space: 3699303325
effective search space used: 3699303325
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)