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= 039586
         (592 letters)

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

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



>pdb|2E4M|A Chain A, Crystal Structure Of Hemagglutinin Subcomponent Complex
           (Ha- 33HA-17) From Clostridium Botulinum Serotype D
           Strain 4947
 pdb|2E4M|B Chain B, Crystal Structure Of Hemagglutinin Subcomponent Complex
           (Ha- 33HA-17) From Clostridium Botulinum Serotype D
           Strain 4947
          Length = 286

 Score = 34.3 bits (77), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 9/73 (12%)

Query: 468 LSDVIGRSVMLELFASPGMLVVRGTDDELVVTDSSSVHGSSIFRLVTRWDGKAETVSLES 527
           L D I R+V+L  + +P +++   TDD L+V  S+  + ++ F        K      E+
Sbjct: 96  LQDYISRNVILRNYMNPNLVLQYNTDDTLIV--STQTNSNNQF-------FKFSNCIYEA 146

Query: 528 VTQKGCFVSTSVN 540
           +  + C + T +N
Sbjct: 147 LNNRNCKLQTQLN 159


>pdb|2BJ1|A Chain A, Nikr In Open Conformation And Nickel Bound To
           High-Affinity Sites
 pdb|2BJ1|B Chain B, Nikr In Open Conformation And Nickel Bound To
           High-Affinity Sites
 pdb|2BJ3|A Chain A, Nikr-Apo
 pdb|2BJ3|B Chain B, Nikr-Apo
 pdb|2BJ3|C Chain C, Nikr-Apo
 pdb|2BJ3|D Chain D, Nikr-Apo
 pdb|2BJ7|A Chain A, Nikr In Closed Conformation And Nickel Bound To High-
           Affinity Sites
 pdb|2BJ7|B Chain B, Nikr In Closed Conformation And Nickel Bound To High-
           Affinity Sites
 pdb|2BJ8|A Chain A, Nikr In Closed Conformation And Nickel Bound To High And
           Low-Affinity Sites
 pdb|2BJ8|B Chain B, Nikr In Closed Conformation And Nickel Bound To High And
           Low-Affinity Sites
 pdb|2BJ9|A Chain A, Nikr With Bound Nickel And Phosphate
 pdb|2BJ9|B Chain B, Nikr With Bound Nickel And Phosphate
          Length = 138

 Score = 30.8 bits (68), Expect = 2.1,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 24/42 (57%)

Query: 118 LLDEYAYADKAEALKITTWMYIVTRHWDSLNEETGGMNDILY 159
           +++E  Y +++EA++     +I+   W+  NEE  G   I+Y
Sbjct: 21  IIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVY 62


  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    0.135    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,342,062
Number of Sequences: 62578
Number of extensions: 780360
Number of successful extensions: 1553
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1551
Number of HSP's gapped (non-prelim): 8
length of query: 592
length of database: 14,973,337
effective HSP length: 104
effective length of query: 488
effective length of database: 8,465,225
effective search space: 4131029800
effective search space used: 4131029800
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)