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= 019366
         (342 letters)

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

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



>pdb|1914|A Chain A, Signal Recognition Particle Alu Rna Binding Heterodimer,
           Srp914
          Length = 232

 Score = 27.7 bits (60), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 24/98 (24%), Positives = 47/98 (47%), Gaps = 10/98 (10%)

Query: 230 KTLQEENDEIGRQNEEGETHQLSVKLALQKSLNAELKSQFEALYKHMDG-----LTDDVE 284
           K + EE+D  G    + +T +   + A +  L   +K +    Y+H+DG     +TDD+ 
Sbjct: 134 KLISEEDDSAGSPMPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDL- 192

Query: 285 RSNEMVLMLREKLEENDHELEKLKHELRQKSVLEEDKN 322
               + L+ R    ++  ++EK   +L +  V +E +N
Sbjct: 193 ----VCLVYRTDQAQDVKKIEKFHSQLMRLMVAKESRN 226


  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
   0.311    0.125    0.335 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,024,473
Number of Sequences: 62578
Number of extensions: 220179
Number of successful extensions: 645
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 625
Number of HSP's gapped (non-prelim): 31
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)