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= psy12187
         (112 letters)

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

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



>pdb|3PNN|A Chain A, The Crystal Structure Of A Glycosyltransferase From
           Porphyromonas Gingivalis W83
          Length = 303

 Score = 26.9 bits (58), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 16/23 (69%)

Query: 87  GTMVYHLRDSFEPEVRKKALARY 109
           G +V+ +R SFE E R+K L +Y
Sbjct: 49  GRLVFVIRHSFEKEFREKILTKY 71


>pdb|2ZF5|O Chain O, Crystal Structure Of Highly Thermostable Glycerol Kinase
           From A Hyperthermophilic Archaeon
 pdb|2ZF5|Y Chain Y, Crystal Structure Of Highly Thermostable Glycerol Kinase
           From A Hyperthermophilic Archaeon
          Length = 497

 Score = 25.8 bits (55), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 6/36 (16%)

Query: 70  FDIRDLDWDDYLETYVRGTMVYHLRDSFEPEVRKKA 105
           F+I+ LDWDD L        ++ + +S  PEVR+ +
Sbjct: 187 FNIKKLDWDDEL------LELFDIPESVLPEVRESS 216


  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
   0.321    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: 3,577,968
Number of Sequences: 62578
Number of extensions: 140986
Number of successful extensions: 335
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 333
Number of HSP's gapped (non-prelim): 4
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)