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= 017036
         (378 letters)

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

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



>pdb|3IGQ|A Chain A, Crystal Structure Of The Extracellular Domain Of A
           Bacterial Pentameric Ligand-Gated Ion Channel
 pdb|3IGQ|B Chain B, Crystal Structure Of The Extracellular Domain Of A
           Bacterial Pentameric Ligand-Gated Ion Channel
 pdb|3IGQ|C Chain C, Crystal Structure Of The Extracellular Domain Of A
           Bacterial Pentameric Ligand-Gated Ion Channel
 pdb|3IGQ|D Chain D, Crystal Structure Of The Extracellular Domain Of A
           Bacterial Pentameric Ligand-Gated Ion Channel
 pdb|3IGQ|E Chain E, Crystal Structure Of The Extracellular Domain Of A
           Bacterial Pentameric Ligand-Gated Ion Channel
 pdb|3IGQ|F Chain F, Crystal Structure Of The Extracellular Domain Of A
           Bacterial Pentameric Ligand-Gated Ion Channel
          Length = 201

 Score = 28.9 bits (63), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 3/75 (4%)

Query: 72  QKRQFGPVPA-WRSEFVEPENIWLIGTTHLSQDSAADVERVVRAIKPDNVVVELCRSRAG 130
           ++  F PV +  R +  EPE IW+     ++ ++A D + V  ++ PD  V  L R  A 
Sbjct: 50  RRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSAR 109

Query: 131 IMYTSNG--GENDQQ 143
           ++   +G   E+D Q
Sbjct: 110 VLSPLDGRRTESDSQ 124


  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    0.135    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,801,115
Number of Sequences: 62578
Number of extensions: 429242
Number of successful extensions: 1015
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1014
Number of HSP's gapped (non-prelim): 15
length of query: 378
length of database: 14,973,337
effective HSP length: 100
effective length of query: 278
effective length of database: 8,715,537
effective search space: 2422919286
effective search space used: 2422919286
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: 52 (24.6 bits)