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= 005852
         (674 letters)

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

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



>pdb|2ZW9|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZW9|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZWA|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZWA|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZZK|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZZK|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
          Length = 695

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)

Query: 376 PAMYIENVTDLAFDDITPEDPDFSSIQGLAEAGL 409
           PAM + NVT+  F D+TP+D  F +   L  AGL
Sbjct: 513 PAMLLYNVTEEIFKDVTPKDEFFQN--SLVSAGL 544


  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
   0.307    0.126    0.336 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,554,306
Number of Sequences: 62578
Number of extensions: 617571
Number of successful extensions: 1317
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1289
Number of HSP's gapped (non-prelim): 27
length of query: 674
length of database: 14,973,337
effective HSP length: 105
effective length of query: 569
effective length of database: 8,402,647
effective search space: 4781106143
effective search space used: 4781106143
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)