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= 018484
         (355 letters)

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

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



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

 Score = 33.5 bits (75), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 52/262 (19%), Positives = 103/262 (39%), Gaps = 34/262 (12%)

Query: 95  GSHGLTKGSLAFLNYPAQIMFKSTKVLPVMIMGAFIPGLRRKYPAHEYVAALLLVFGLIL 154
           G   +   +   L+Y  +IM+      P  I  ++   +   +P  +    + L  G+  
Sbjct: 98  GDFAIVHMTKLLLDYTGKIMWT-----PPAIFKSYCEIIVTHFPFDQQNCTMKL--GIWT 150

Query: 155 FTMADAQTSPNFSL--IGVLMISGALVMDSFLGNLQEVIFTVNPDTTQMEMLFCSTVVGL 212
           +       SP      +   M SG  VM  + G    V +T  PDT  +++ +   +  +
Sbjct: 151 YDGTKVSISPESDRPDLSTFMESGEWVMKDYRGWKHWVYYTCCPDTPYLDITYHFIMQRI 210

Query: 213 PFLLVPMILTGELVRAWNSCSQHLYVYGVLVF----EAMATFVGQVSVLSLIALFGAATT 268
           P   V  ++   L+ ++ +         VLVF    ++       +SVL  + +F     
Sbjct: 211 PLYFVVNVIIPCLLFSFLT---------VLVFYLPTDSGEKMTLSISVLLSLTVFLLVIV 261

Query: 269 AMITTARKAVTLFLSYLIFTKPLTEQHGTGLLLIAMGIILKMLPENKAPANNRPNSHNNV 328
            +I +   AV L   Y++FT          ++ +   II+ ++  N    +  P++H+ +
Sbjct: 262 ELIPSTSSAVPLIGKYMLFT----------MIFVISSIIVTVVVINT--HHRSPSTHSAI 309

Query: 329 KRRKSPEPEEKSLVETNGEVEE 350
           +  K      KS  E++   EE
Sbjct: 310 EGVKYIAEHMKSDEESSNAAEE 331


>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
          Length = 751

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 8/42 (19%)

Query: 13  VSLSDRPRWQQFLICSSGFFFGYLVNGICEEYVYNRLQFSYG 54
           VS  D+ RW+    C+      Y VN + EE++YN L  SYG
Sbjct: 99  VSFIDQRRWK----CN----LCYRVNDVPEEFMYNPLTRSYG 132


>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 = 29.6 bits (65), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 41/200 (20%), Positives = 78/200 (39%), Gaps = 22/200 (11%)

Query: 95  GSHGLTKGSLAFLNYPAQIMFKSTKVLPVMIMGAFIPGLRRKYPAHEYVAALLLVFGLIL 154
           G   +   +   L+Y  +IM+      P  I  ++   +   +P  +    + L  G+  
Sbjct: 122 GDFAIVHMTKLLLDYTGKIMWT-----PPAIFKSYCEIIVTHFPFDQQNCTMKL--GIWT 174

Query: 155 FTMADAQTSPNFSL--IGVLMISGALVMDSFLGNLQEVIFTVNPDTTQMEMLFCSTVVGL 212
           +       SP      +   M SG  VM  + G    V +T  PDT  +++ +   +  +
Sbjct: 175 YDGTKVSISPESDRPDLSTFMESGEWVMKDYRGWKHWVYYTCCPDTPYLDITYHFIMQRI 234

Query: 213 PFLLVPMILTGELVRAWNSCSQHLYVYGVLVF----EAMATFVGQVSVLSLIALFGAATT 268
           P   V  ++   L+ ++ +         VLVF    ++       +SVL  + +F     
Sbjct: 235 PLYFVVNVIIPCLLFSFLT---------VLVFYLPTDSGEKMTLSISVLLSLTVFLLVIV 285

Query: 269 AMITTARKAVTLFLSYLIFT 288
            +I +   AV L   Y++FT
Sbjct: 286 ELIPSTSSAVPLIGKYMLFT 305


>pdb|1THG|A Chain A, 1.8 Angstroms Refined Structure Of The Lipase From
           Geotrichum Candidum
          Length = 544

 Score = 27.7 bits (60), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 116 KSTKVLPVMIM---GAFIPGLRRKYPAHEYVAALLLVFGLILFTMADAQTSPNFSLIGVL 172
           K    LPVM+    GAF+ G    YP + YV   + +   ++F   + +T P F  +G  
Sbjct: 117 KPDAKLPVMVWIYGGAFVYGSSAAYPGNSYVKESINMGQPVVFVSINYRTGP-FGFLGGD 175

Query: 173 MIS 175
            I+
Sbjct: 176 AIT 178


  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
   0.325    0.139    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,652,660
Number of Sequences: 62578
Number of extensions: 365349
Number of successful extensions: 847
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 846
Number of HSP's gapped (non-prelim): 5
length of query: 355
length of database: 14,973,337
effective HSP length: 100
effective length of query: 255
effective length of database: 8,715,537
effective search space: 2222461935
effective search space used: 2222461935
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)