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= 027153
         (227 letters)

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

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



>pdb|3O0R|B Chain B, Crystal Structure Of Nitric Oxide Reductase From
           Pseudomonas Aeruginosa In Complex With Antibody Fragment
          Length = 465

 Score = 27.3 bits (59), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 25/121 (20%), Positives = 56/121 (46%), Gaps = 17/121 (14%)

Query: 123 ISMAIVSVVWLAAAVCFFVALPNHSWLWLINFFNAIQVI----MTLIKY--IPQAIMNFR 176
           I+MA++S +       F++ +P + WLWL + F+A++ +    M L  +  I +   ++ 
Sbjct: 245 IAMALISGIIGTGHHYFWIGVPGY-WLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYP 303

Query: 177 RKSTDGFSIGNILLDFLGGC----------TNYSQMIVQSIDQNSWVNFYGNIGKTLLSL 226
            ++   +++G  ++ FLG             NY     Q    +  + FYG     ++++
Sbjct: 304 NRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTI 363

Query: 227 V 227
           +
Sbjct: 364 I 364


  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    0.139    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,239,726
Number of Sequences: 62578
Number of extensions: 214102
Number of successful extensions: 491
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 491
Number of HSP's gapped (non-prelim): 1
length of query: 227
length of database: 14,973,337
effective HSP length: 95
effective length of query: 132
effective length of database: 9,028,427
effective search space: 1191752364
effective search space used: 1191752364
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: 50 (23.9 bits)