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= 028679
         (205 letters)

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

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



>pdb|1CIY|A Chain A, Insecticidal Toxin: Structure And Channel Formation
          Length = 590

 Score = 32.0 bits (71), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 29/123 (23%), Positives = 48/123 (39%), Gaps = 17/123 (13%)

Query: 52  LYGNKGDQMAPVMGGLGGTLLVRKLPAADPKRVSVG------DVVVMKDPEKSDNYIVRR 105
           L+GN G+   PV+  L G  + R L +   +R+ +G      ++ V+   E S   +   
Sbjct: 309 LFGNAGNAAPPVLVSLTGLGIFRTLSSPLYRRIILGSGPNNQELFVLDGTEFSFASLTTN 368

Query: 106 LAAIEGYEMVSTDEKDEPFVLDKDECWVLADNENMKPKEANDSRTFGPVPMRNIVGRAIY 165
           L +    +  + D  D           V+   +N  P  A  S     V M +    A+Y
Sbjct: 369 LPSTIYRQRGTVDSLD-----------VIPPQDNSVPPRAGFSHRLSHVTMLSQAAGAVY 417

Query: 166 CLR 168
            LR
Sbjct: 418 TLR 420


  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    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,440,654
Number of Sequences: 62578
Number of extensions: 266987
Number of successful extensions: 599
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 599
Number of HSP's gapped (non-prelim): 1
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
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: 49 (23.5 bits)