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= psy12608
         (65 letters)

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

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



>pdb|1DPE|A Chain A, Dipeptide-Binding Protein
          Length = 507

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 20  PLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAA 51
           PLD +K R    Y   +    KA+Y+G G +A
Sbjct: 275 PLDDVKVRQALTYAVNKDAIIKAVYQGAGVSA 306


>pdb|1DPP|A Chain A, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
 pdb|1DPP|C Chain C, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
 pdb|1DPP|E Chain E, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
 pdb|1DPP|G Chain G, Dipeptide Binding Protein Complex With Glycyl-L-Leucine
          Length = 507

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 20  PLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAA 51
           PLD +K R    Y   +    KA+Y+G G +A
Sbjct: 275 PLDDVKVRQALTYAVNKDAIIKAVYQGAGVSA 306


>pdb|3M8U|A Chain A, Crystal Structure Of Glutathione-Binding Protein A (Gbpa)
           From Haemophilus Parasuis Sh0165 In Complex With
           Glutathione Disulfide (Gssg)
          Length = 522

 Score = 25.4 bits (54), Expect = 9.1,   Method: Composition-based stats.
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 20  PLDTIKTRLQSQYGFWRSGGFKAIYKGLGPAA 51
           P D +K R    Y   ++    A+Y+G G AA
Sbjct: 277 PFDNVKVRQALNYAVDKNAIIDAVYRGAGVAA 308


  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    0.142    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,382,954
Number of Sequences: 62578
Number of extensions: 35380
Number of successful extensions: 116
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 113
Number of HSP's gapped (non-prelim): 4
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)