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= psy8501
         (195 letters)

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

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



>pdb|1NYQ|A Chain A, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With An Analogue Of Threonyl
           Adenylate
 pdb|1NYQ|B Chain B, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With An Analogue Of Threonyl
           Adenylate
 pdb|1NYR|A Chain A, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With Atp
 pdb|1NYR|B Chain B, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With Atp
          Length = 645

 Score = 27.7 bits (60), Expect = 4.7,   Method: Composition-based stats.
 Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 108 KYVYGIVAFGYMPILYAVIYYFHDFWTYITLDPDEDIEDKEITMWQ 153
           K +YG V FG  P++    YY  D    I+ D   D E  E TM Q
Sbjct: 86  KRLYGNVKFGVGPVIEGGFYYDFDIDQNISSD---DFEQIEKTMKQ 128


  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
   0.330    0.141    0.468 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,070,516
Number of Sequences: 62578
Number of extensions: 174076
Number of successful extensions: 371
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 369
Number of HSP's gapped (non-prelim): 2
length of query: 195
length of database: 14,973,337
effective HSP length: 94
effective length of query: 101
effective length of database: 9,091,005
effective search space: 918191505
effective search space used: 918191505
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 bits)