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= 026388
         (239 letters)

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

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



>pdb|1JC5|A Chain A, Crystal Structure Of Native Methylmalonyl-Coa Epimerase
 pdb|1JC5|B Chain B, Crystal Structure Of Native Methylmalonyl-Coa Epimerase
 pdb|1JC5|C Chain C, Crystal Structure Of Native Methylmalonyl-Coa Epimerase
 pdb|1JC5|D Chain D, Crystal Structure Of Native Methylmalonyl-Coa Epimerase
 pdb|1JC5|E Chain E, Crystal Structure Of Native Methylmalonyl-Coa Epimerase
 pdb|1JC5|F Chain F, Crystal Structure Of Native Methylmalonyl-Coa Epimerase
          Length = 148

 Score = 29.6 bits (65), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 7  YLQES-GWEELRKEARKIEGDLDVKLSSYAKLGARFTQ 43
          Y QE+ GW EL +E    +G +++ ++  AKL    TQ
Sbjct: 26 YYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQ 63


>pdb|4B19|A Chain A, S. Aureus Pepa1 Nmr Structure
          Length = 30

 Score = 28.1 bits (61), Expect = 4.6,   Method: Composition-based stats.
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 220 ILAAVIAGCTLFLIIYWLSK 239
           I+A VI+GC +    YWLS+
Sbjct: 7   IIAPVISGCAIAFFSYWLSR 26


>pdb|1JC4|A Chain A, Crystal Structure Of Se-Met Methylmalonyl-Coa Epimerase
 pdb|1JC4|B Chain B, Crystal Structure Of Se-Met Methylmalonyl-Coa Epimerase
 pdb|1JC4|C Chain C, Crystal Structure Of Se-Met Methylmalonyl-Coa Epimerase
 pdb|1JC4|D Chain D, Crystal Structure Of Se-Met Methylmalonyl-Coa Epimerase
          Length = 148

 Score = 27.7 bits (60), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 7  YLQES-GWEELRKEARKIEGDLDVKLSSYAKLGARFTQ 43
          Y QE+ GW EL +E    +G +++  +  AKL    TQ
Sbjct: 26 YYQETFGWHELHREENPEQGVVEIXXAPAAKLTEHXTQ 63


  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
   0.318    0.132    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,118,933
Number of Sequences: 62578
Number of extensions: 216238
Number of successful extensions: 562
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 557
Number of HSP's gapped (non-prelim): 8
length of query: 239
length of database: 14,973,337
effective HSP length: 96
effective length of query: 143
effective length of database: 8,965,849
effective search space: 1282116407
effective search space used: 1282116407
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)