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= 025989
         (245 letters)

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

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



>pdb|1DBI|A Chain A, Crystal Structure Of A Thermostable Serine Protease
          Length = 280

 Score = 28.9 bits (63), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 50  AAAPLSHAVGLISPLPSTRFCQIRCRANRSGNSAYSPLNSGSNFSDRPPTEMAPLFPGCD 109
           AAA  ++A G+    P+TR   +R   +R+G+   S +     ++     E+  L  GCD
Sbjct: 80  AAAETNNATGIAGMAPNTRILAVRAL-DRNGSGTLSDIADAIIYAADSGAEVINLSLGCD 138


>pdb|2NN6|C Chain C, Structure Of The Human Rna Exosome Composed Of Rrp41,
           Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
          Length = 278

 Score = 28.1 bits (61), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 109 DYEHWLIVMDKPGGEGATKQQMIDCYIKTLAQVVGSEEEAKKKIYNV 155
           D E  L  + KPGG G T  ++ DC    +++ V   +E KK +  V
Sbjct: 229 DEEGKLCCLHKPGGSGLTGAKLQDC----MSRAVTRHKEVKKLMDEV 271


  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
   0.316    0.134    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,010,198
Number of Sequences: 62578
Number of extensions: 259153
Number of successful extensions: 457
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 457
Number of HSP's gapped (non-prelim): 2
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)