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= psy15627
         (77 letters)

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

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



>pdb|1A0D|A Chain A, Xylose Isomerase From Bacillus Stearothermophilus
 pdb|1A0D|B Chain B, Xylose Isomerase From Bacillus Stearothermophilus
 pdb|1A0D|C Chain C, Xylose Isomerase From Bacillus Stearothermophilus
 pdb|1A0D|D Chain D, Xylose Isomerase From Bacillus Stearothermophilus
          Length = 440

 Score = 26.9 bits (58), Expect = 2.7,   Method: Composition-based stats.
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 41  ERPMCVSSSRVDWNTSHAFRHTPFVKG 67
           E  M  S +++ WNT++ F H  FV G
Sbjct: 124 EEYMKTSKTKLLWNTANLFTHPRFVHG 150


>pdb|2LX4|A Chain A, Nmr Solution Structure Of Peptide A2n(1-17) From Mus
          Musculus V-atpase
          Length = 17

 Score = 26.9 bits (58), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/17 (64%), Positives = 14/17 (82%)

Query: 1  MGAMFRSEEMALCQLFI 17
          MG++FRSE M L QLF+
Sbjct: 1  MGSLFRSESMCLAQLFL 17


>pdb|4DNH|A Chain A, Crystal Structure Of Hypothetical Protein Smc04132 From
          Sinorhizobium Meliloti 1021
          Length = 396

 Score = 25.8 bits (55), Expect = 5.9,   Method: Composition-based stats.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 51 VDWNTSHAFRHTPFVKGLGIA 71
          +DW  + AFRH  +  GLG+A
Sbjct: 59 IDWERTLAFRHRLWDLGLGVA 79


  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
   0.322    0.134    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,106,576
Number of Sequences: 62578
Number of extensions: 62910
Number of successful extensions: 109
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 106
Number of HSP's gapped (non-prelim): 3
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)