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= psy17040
         (354 letters)

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

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



>pdb|3J0A|A Chain A, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
           An Electron Microscopy Single Particle Reconstruction
 pdb|3J0A|B Chain B, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
           An Electron Microscopy Single Particle Reconstruction
          Length = 844

 Score = 29.6 bits (65), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 26/113 (23%), Positives = 54/113 (47%), Gaps = 16/113 (14%)

Query: 19  PDVYLGFISTITWIVLFLTISMLVITSSTLFSPRVMLFIFALPVMQVIL-----FCLAIG 73
           PD++L     +T   + LT +++ ++ + L +  ++ F+  +P +Q+++     F    G
Sbjct: 384 PDIFLSGNKLVTLPKINLTANLIHLSENRLENLDILYFLLRVPHLQILILNQNRFSSCSG 443

Query: 74  -----RDPTGLHLAIVNQ--EMDWATKAC----PVLSNCSFTHLSCRYLNSLP 115
                 +P+   L +     ++ W T+ C      LS+    +L+  YLNSLP
Sbjct: 444 DQTPSENPSLEQLFLGENMLQLAWETELCWDVFEGLSHLQVLYLNHNYLNSLP 496


>pdb|2XVG|A Chain A, Crystal Structure Of Alpha-Xylosidase (Gh31) From
           Cellvibrio Japonicus
 pdb|2XVK|A Chain A, Crystal Structure Of Alpha-Xylosidase (Gh31) From
           Cellvibrio Japonicus In Complex With
           5-Fluoro-Alpha-D-Xylopyranosyl Fluoride
 pdb|2XVL|A Chain A, Crystal Structure Of Alpha-Xylosidase (Gh31) From
           Cellvibrio Japonicus In Complex With Pentaerythritol
           Propoxylate (5 4 Po Oh)
          Length = 1020

 Score = 29.6 bits (65), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 7/56 (12%)

Query: 121 KDYYPDPESAINAVRVGDA------WGALY-FTDNFTDALVARMVLGRDADEETLD 169
           K ++PDP++ ++ V   +A      W   Y  TDN+ +      +  R+ DE+ LD
Sbjct: 486 KQFFPDPKALVDKVHAMNAQIMISVWPKFYPTTDNYKELNAKGFMFNRNLDEKNLD 541


  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    0.142    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,981,040
Number of Sequences: 62578
Number of extensions: 384818
Number of successful extensions: 1603
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1599
Number of HSP's gapped (non-prelim): 7
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)