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= psy4519
         (236 letters)

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

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



>pdb|1IVH|A Chain A, Structure Of Human Isovaleryl-coa Dehydrogenase At 2.6
           Angstroms Resolution: Structural Basis For Substrate
           Specificity
 pdb|1IVH|B Chain B, Structure Of Human Isovaleryl-coa Dehydrogenase At 2.6
           Angstroms Resolution: Structural Basis For Substrate
           Specificity
 pdb|1IVH|C Chain C, Structure Of Human Isovaleryl-coa Dehydrogenase At 2.6
           Angstroms Resolution: Structural Basis For Substrate
           Specificity
 pdb|1IVH|D Chain D, Structure Of Human Isovaleryl-coa Dehydrogenase At 2.6
           Angstroms Resolution: Structural Basis For Substrate
           Specificity
          Length = 394

 Score = 31.2 bits (69), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 42/95 (44%), Gaps = 23/95 (24%)

Query: 118 RYWDALSHMIKGALGTGILTMPHAFKDSGYLLGFLGTVAI---------------GAFTT 162
            +W  L ++  G LG   +T P  +  SG  LG+L  V +               GA + 
Sbjct: 50  EFWKQLGNL--GVLG---ITAPVQYGGSG--LGYLEHVLVMEEISRASGAVGLSYGAHSN 102

Query: 163 SCIQILVRAQYELCRRKRIPSLTYPEILGA-ALSE 196
            CI  LVR   E  + K +P L   E +GA A+SE
Sbjct: 103 LCINQLVRNGNEAQKEKYLPKLISGEYIGALAMSE 137


>pdb|3S81|A Chain A, Crystal Structure Of Putative Aspartate Racemase From
           Salmonella Typhimurium
 pdb|3S81|B Chain B, Crystal Structure Of Putative Aspartate Racemase From
           Salmonella Typhimurium
 pdb|3S81|C Chain C, Crystal Structure Of Putative Aspartate Racemase From
           Salmonella Typhimurium
 pdb|3S81|D Chain D, Crystal Structure Of Putative Aspartate Racemase From
           Salmonella Typhimurium
          Length = 268

 Score = 27.3 bits (59), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 16/94 (17%)

Query: 140 HAFKDSGYLLGFLGTVAIGAFTTSCIQILVRAQYELCRRKRIPSL-----TYPEILGAAL 194
           +A K +  +LG +G  A    T   ++  V  ++  C ++ IP +       P+     L
Sbjct: 23  NAMKHTIGILGGMGPAA----TADMLEKFVELRHASCDQQHIPLIVSSIPDIPDRTACLL 78

Query: 195 SEGPARFRWLAPYGRGLSFTAMIVDEIGALCVYL 228
           S GP+ +R+L  Y         ++++ GA C+ +
Sbjct: 79  SGGPSPYRYLERY-------LHMLEDAGAECIVI 105


  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
   0.327    0.142    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,899,995
Number of Sequences: 62578
Number of extensions: 270572
Number of successful extensions: 1056
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1050
Number of HSP's gapped (non-prelim): 10
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)