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= psy1968
         (215 letters)

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

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



>pdb|3PSF|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(236-1259)
          Length = 1030

 Score = 28.1 bits (61), Expect = 3.3,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 2/31 (6%)

Query: 167 SDHIVYEPLDHPTNLPVRLRSPSTVFNGQSG 197
           S H ++ P+DHP++ PV +    ++ N  SG
Sbjct: 301 SQHQIHPPVDHPSSKPVEV--IESILNANSG 329


>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(239-1451)
          Length = 1219

 Score = 28.1 bits (61), Expect = 3.5,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 2/31 (6%)

Query: 167 SDHIVYEPLDHPTNLPVRLRSPSTVFNGQSG 197
           S H ++ P+DHP++ PV +    ++ N  SG
Sbjct: 298 SQHQIHPPVDHPSSKPVEV--IESILNANSG 326


>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 = 27.7 bits (60), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 24/96 (25%)

Query: 78  GLSPKSVCAVPAASDYPETYLRNTDKEKLLIWYCENFRRQYSSRYPLRRPLVMALENECG 137
           G+ P+    +P  SD             L+IWY ++ +++Y+S+  L    +M  E+ C 
Sbjct: 432 GMYPQKGSILPGVSD-----------ADLVIWYPDDSKKEYNSKPKLITNKLM--EHNC- 477

Query: 138 VQKMVCTSINVTRFPLVEFKSWSGCASFVSDHIVYE 173
                    + T F  +E K+W    + V   IVY+
Sbjct: 478 ---------DYTPFEGIEIKNWPRY-TIVKGKIVYK 503


  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
   0.320    0.136    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,644,417
Number of Sequences: 62578
Number of extensions: 206295
Number of successful extensions: 379
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: 379
Number of HSP's gapped (non-prelim): 3
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)