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= 028822
         (203 letters)

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

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



>pdb|4AQ5|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ9|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
          Length = 488

 Score = 27.3 bits (59), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 1/40 (2%)

Query: 75  IERLHLAHFHVRMKPAICIDISLNVTLKVHNRDVYSVNYK 114
           IE+L L  +  R+KPA  +D  ++VTLK+   ++ S+N K
Sbjct: 7   IEKL-LGDYDKRIKPAKTLDHVIDVTLKLTLTNLISLNEK 45


>pdb|2BG9|E Chain E, Refined Structure Of The Nicotinic Acetylcholine Receptor
           At 4a Resolution
          Length = 370

 Score = 26.6 bits (57), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 1/40 (2%)

Query: 75  IERLHLAHFHVRMKPAICIDISLNVTLKVHNRDVYSVNYK 114
           IE+L L  +  R+KPA  +D  ++VTLK+   ++ S+N K
Sbjct: 7   IEKL-LGDYDKRIKPAKTLDHVIDVTLKLTLTNLISLNEK 45


  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
   0.321    0.138    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,968,435
Number of Sequences: 62578
Number of extensions: 219688
Number of successful extensions: 373
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 373
Number of HSP's gapped (non-prelim): 6
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)