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= psy16958
         (257 letters)

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

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



>pdb|2ZKR|LL Chain l, Structure Of A Mammalian Ribosomal 60s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 148

 Score = 31.6 bits (70), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 10/94 (10%)

Query: 3   QNPKNPGYEATIHHPPQSNINFNRKHKP--TSTRFKQYFTDANINLTNTAYMKQSIPPWT 60
           ++P   G    +HH     INF++ H         K Y    N +   T  + +   PWT
Sbjct: 27  KHPGGRGNAGGMHH---HRINFDKYHPGYFGKVGMKHYHLKRNQSFCPTVNLDK---PWT 80

Query: 61  ITLPETQLLLKEKKTNISP--NEIKSKFNQLLNK 92
           +   +T++   + KT ++P  + ++S + ++L K
Sbjct: 81  LVSEQTRVNAAKNKTGVAPIIDVVRSGYYKVLGK 114


  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
   0.317    0.132    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,192,145
Number of Sequences: 62578
Number of extensions: 261275
Number of successful extensions: 560
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: 559
Number of HSP's gapped (non-prelim): 3
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)