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= psy18229
         (111 letters)

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

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



>pdb|4AQ5|B Chain B, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ9|B Chain B, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
          Length = 493

 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 25/33 (75%)

Query: 16  NYHHRTADSHEMPDWIRFLFLQWIPWILCMQRP 48
           N HHR+ ++H MP+WIR +F++ +P  L +QRP
Sbjct: 327 NLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRP 359


>pdb|1OED|B Chain B, Structure Of Acetylcholine Receptor Pore From Electron
           Images
          Length = 250

 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 25/33 (75%)

Query: 16  NYHHRTADSHEMPDWIRFLFLQWIPWILCMQRP 48
           N HHR+ ++H MP+WIR +F++ +P  L +QRP
Sbjct: 87  NLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRP 119


>pdb|1OED|A Chain A, Structure Of Acetylcholine Receptor Pore From Electron
           Images
 pdb|1OED|D Chain D, Structure Of Acetylcholine Receptor Pore From Electron
           Images
          Length = 227

 Score = 37.0 bits (84), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 3/39 (7%)

Query: 16  NYHHRTADSHEMPDWIRFLFLQWIPWIL---CMQRPHKK 51
           N HHR+  +H MP W+R +F+  IP ++    M+R  K+
Sbjct: 87  NTHHRSPSTHTMPQWVRKIFIDTIPNVMFFSTMKRASKE 125


>pdb|4AQ5|A Chain A, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ5|D Chain D, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ9|A Chain A, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
 pdb|4AQ9|D Chain D, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
          Length = 461

 Score = 35.8 bits (81), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 16  NYHHRTADSHEMPDWIRFLFLQWIPWIL---CMQRPHK-KITRKTIAMSNKMRELELKER 71
           N HHR+  +H MP W+R +F+  IP ++    M+R  K K   K  A    + ++  K+ 
Sbjct: 321 NTHHRSPSTHTMPQWVRKIFINTIPNVMFFSTMKRASKEKQENKIFADDIDISDISGKQV 380

Query: 72  TSKSLMANVLNIDDDFR 88
           T + +    L  + D +
Sbjct: 381 TGEVIFQTPLIKNPDVK 397


>pdb|4AQ5|C Chain C, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ9|C Chain C, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
          Length = 522

 Score = 29.6 bits (65), Expect = 0.49,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 20/32 (62%)

Query: 16  NYHHRTADSHEMPDWIRFLFLQWIPWILCMQR 47
           N+H RT  +H +   ++ +FL+ +P IL M R
Sbjct: 332 NFHFRTPSTHVLSTRVKQIFLEKLPRILHMSR 363


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

 Score = 29.3 bits (64), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 20/32 (62%)

Query: 16  NYHHRTADSHEMPDWIRFLFLQWIPWILCMQR 47
           N+H RT  +H +   ++ +FL+ +P IL M R
Sbjct: 87  NFHFRTPSTHVLSTRVKQIFLEKLPRILHMSR 118


  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
   0.328    0.134    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,433,718
Number of Sequences: 62578
Number of extensions: 62746
Number of successful extensions: 120
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 112
Number of HSP's gapped (non-prelim): 8
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)