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= psy2736
         (211 letters)

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

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



>pdb|2FTY|A Chain A, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri
 pdb|2FTY|B Chain B, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri
 pdb|2FTY|C Chain C, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri
 pdb|2FTY|D Chain D, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri
 pdb|2FVK|A Chain A, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Substrate
           Dihydrouracil
 pdb|2FVK|B Chain B, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Substrate
           Dihydrouracil
 pdb|2FVK|C Chain C, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Substrate
           Dihydrouracil
 pdb|2FVK|D Chain D, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Substrate
           Dihydrouracil
 pdb|2FVM|A Chain A, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Reaction
           Product N-carbamyl-beta-alanine
 pdb|2FVM|B Chain B, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Reaction
           Product N-carbamyl-beta-alanine
 pdb|2FVM|C Chain C, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Reaction
           Product N-carbamyl-beta-alanine
 pdb|2FVM|D Chain D, Crystal Structure Of Dihydropyrimidinase From
           Saccharomyces Kluyveri In Complex With The Reaction
           Product N-carbamyl-beta-alanine
          Length = 559

 Score = 30.8 bits (68), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 8/66 (12%)

Query: 139 IPVVVDCSHIYGADFTAAKVIEVLCQNFSRRGQPLFFFNLKPSVVAVFEGVQPKDFVVYY 198
           +P++ D  ++ G   +  K++E+ C N      P   + + P   ++  GV   D V++Y
Sbjct: 400 MPLLYDYGYLRGNLTSMMKLVEIQCTN------PAKVYGMYPQKGSILPGVSDADLVIWY 453

Query: 199 --DSRE 202
             DS++
Sbjct: 454 PDDSKK 459


>pdb|1YKW|A Chain A, Crystal Structure Of A Novel Rubisco-Like Protein From The
           Green Sulfur Bacterium Chlorobium Tepidum
 pdb|1YKW|B Chain B, Crystal Structure Of A Novel Rubisco-Like Protein From The
           Green Sulfur Bacterium Chlorobium Tepidum
          Length = 435

 Score = 29.6 bits (65), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 10/62 (16%)

Query: 138 GIPVV----VDCSHIYGADFTAAKV-IEVLCQNFSRRGQPLFFFNLKPSVVAVFEGVQPK 192
           G+PVV    +     Y ADF   K  IE L    +  G+P+FF  +KP++     G+ P 
Sbjct: 126 GVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAHGRPIFFGVVKPNI-----GLSPG 180

Query: 193 DF 194
           +F
Sbjct: 181 EF 182


>pdb|1TEL|A Chain A, Crystal Structure Of A Rubisco-Like Protein From
           Chlorobium Tepidum
 pdb|1TEL|B Chain B, Crystal Structure Of A Rubisco-Like Protein From
           Chlorobium Tepidum
          Length = 435

 Score = 29.6 bits (65), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 10/62 (16%)

Query: 138 GIPVV----VDCSHIYGADFTAAKV-IEVLCQNFSRRGQPLFFFNLKPSVVAVFEGVQPK 192
           G+PVV    +     Y ADF   K  IE L    +  G+P+FF  +KP++     G+ P 
Sbjct: 126 GVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAHGRPIFFGVVKPNI-----GLSPG 180

Query: 193 DF 194
           +F
Sbjct: 181 EF 182


  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
   0.323    0.136    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,687,571
Number of Sequences: 62578
Number of extensions: 210627
Number of successful extensions: 436
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 436
Number of HSP's gapped (non-prelim): 3
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)