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= 042390
         (626 letters)

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

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



>pdb|1ZJR|A Chain A, Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODIFYING
           ENZYME
          Length = 211

 Score = 29.6 bits (65), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 48/96 (50%), Gaps = 12/96 (12%)

Query: 263 NFQQ---SQPTS--VGDDLELSEPENNGTSDVNEISIETDSHQSQ-------IVQSDAPS 310
           NF++   ++PT   VG++L+   PE    +D   +       QS        I+  +A  
Sbjct: 111 NFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQR 170

Query: 311 QQELKSLSNKPEMESEPPKRSMKRFASEDLETEGKK 346
           Q+E K + ++P +  E  ++ +K++A ED+  E K+
Sbjct: 171 QREEKGMYSRPSLSEEEIQKILKKWAYEDVIKERKR 206


  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    0.124    0.344 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,341,721
Number of Sequences: 62578
Number of extensions: 675707
Number of successful extensions: 1211
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1206
Number of HSP's gapped (non-prelim): 11
length of query: 626
length of database: 14,973,337
effective HSP length: 105
effective length of query: 521
effective length of database: 8,402,647
effective search space: 4377779087
effective search space used: 4377779087
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: 54 (25.4 bits)