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= 003359
         (827 letters)

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

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



>pdb|1N80|A Chain A, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N80|B Chain B, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N80|C Chain C, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N80|D Chain D, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N8B|A Chain A, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N8B|B Chain B, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N8B|C Chain C, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1N8B|D Chain D, Bacteriophage T4 Baseplate Structural Protein Gp8
 pdb|1PDM|A Chain A, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|B Chain B, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|C Chain C, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|D Chain D, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|E Chain E, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|F Chain F, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|G Chain G, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|H Chain H, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|I Chain I, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|J Chain J, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|K Chain K, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1PDM|L Chain L, Fitting Of Gp8 Structure Into The Cryoem Reconstruction
          Of The Bacteriophage T4 Baseplate
 pdb|1TJA|A Chain A, Fitting Of Gp8, Gp9, And Gp11 Into The Cryo-em
          Reconstruction Of The Bacteriophage T4 Contracted Tail
 pdb|1TJA|B Chain B, Fitting Of Gp8, Gp9, And Gp11 Into The Cryo-em
          Reconstruction Of The Bacteriophage T4 Contracted Tail
          Length = 334

 Score = 32.0 bits (71), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 24 PPSPVDEVINLLDKVEHLLANVEQAPSRSMRDALLP 59
          PP P D V+ + D   H++  V+  P  SM DA++P
Sbjct: 58 PPYPTDSVLGVTDMWTHMMGTVKVLP--SMLDAVIP 91


>pdb|2NYG|A Chain A, Crystal Structure Of Yokd Protein From Bacillus Subtilis
 pdb|2NYG|B Chain B, Crystal Structure Of Yokd Protein From Bacillus Subtilis
 pdb|2NYG|C Chain C, Crystal Structure Of Yokd Protein From Bacillus Subtilis
 pdb|2NYG|D Chain D, Crystal Structure Of Yokd Protein From Bacillus Subtilis
 pdb|2NYG|E Chain E, Crystal Structure Of Yokd Protein From Bacillus Subtilis
 pdb|2NYG|F Chain F, Crystal Structure Of Yokd Protein From Bacillus Subtilis
          Length = 273

 Score = 30.4 bits (67), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 18/24 (75%)

Query: 153 VVEMFQHFLKVIRSNHPHFVFAAM 176
           +VE+F+ + +V RSNHP++ F A 
Sbjct: 115 IVELFRSYPEVKRSNHPNYSFVAW 138


  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
   0.310    0.128    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,524,233
Number of Sequences: 62578
Number of extensions: 879210
Number of successful extensions: 1650
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1649
Number of HSP's gapped (non-prelim): 5
length of query: 827
length of database: 14,973,337
effective HSP length: 107
effective length of query: 720
effective length of database: 8,277,491
effective search space: 5959793520
effective search space used: 5959793520
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 bits)