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= 031143
         (165 letters)

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

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



>pdb|3UYC|A Chain A, Designed Protein Ke59 R8_27A
 pdb|3UYC|B Chain B, Designed Protein Ke59 R8_27A
          Length = 249

 Score = 29.6 bits (65), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 72  IVDGVHRLES-EANKYTQEELILMKTQDIGYILQKLQSERNKIEKL 116
           I+   H LE+ E NK  Q +LI M   D+  ++    SERN+IE+L
Sbjct: 177 IIISSHDLETLEINKENQRKLISMVPSDVVKVVASGISERNEIEEL 222


>pdb|1OED|E Chain E, Structure Of Acetylcholine Receptor Pore From Electron
           Images
          Length = 260

 Score = 27.7 bits (60), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 9   PRRAHKERAQPQSRKKFGLLEKHKDYVVR 37
           P     E+ QP+ R  FG++ K ++Y+++
Sbjct: 121 PSEETPEKPQPRRRSSFGIMIKAEEYILK 149


>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 = 27.7 bits (60), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 9   PRRAHKERAQPQSRKKFGLLEKHKDYVVR 37
           P     E+ QP+ R  FG++ K ++Y+++
Sbjct: 338 PSEETPEKPQPRRRSSFGIMIKAEEYILK 366


>pdb|3UY8|A Chain A, Designed Protein Ke59 R5_115F
 pdb|3UY8|B Chain B, Designed Protein Ke59 R5_115F
          Length = 247

 Score = 27.7 bits (60), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 72  IVDGVHRLES-EANKYTQEELILMKTQDIGYILQKLQSERNKIEKL 116
           I+   H LE+ E NK  Q +LI M   ++  ++    SERN+IE+L
Sbjct: 176 IIISSHDLETLEINKENQRKLISMIPSNVVKVVASGISERNEIEEL 221


  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
   0.319    0.133    0.361 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,241,982
Number of Sequences: 62578
Number of extensions: 152427
Number of successful extensions: 536
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 521
Number of HSP's gapped (non-prelim): 26
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)