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= 023353
         (283 letters)

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

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



>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
           And T399i In Complex With Md-2 And Lps
 pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
           And T399i In Complex With Md-2 And Lps
          Length = 635

 Score = 28.5 bits (62), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 56/131 (42%), Gaps = 19/131 (14%)

Query: 77  WIPCVFAMGLLFFMGVEYTLRMVPDSSP----PFDLGFIATRPLHRLLSSS----PQLNT 128
           W PCV  +  + +  +E     +PD+ P      DL F    PL  L S S    P+L  
Sbjct: 24  WEPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSF---NPLRHLGSYSFFSFPELQV 80

Query: 129 LF---AALNTAFVG-MQTAYILWTWLIEGRPRATISALFMFTFRGILGYSTQLPLPQGFL 184
           L      + T   G  Q+   L T ++ G P   I +L +  F G L    +L   +  L
Sbjct: 81  LDLSRCEIQTIEDGAYQSLSHLSTLILTGNP---IQSLALGAFSG-LSSLQKLVAVETNL 136

Query: 185 GSGMDFPVGNV 195
            S  +FP+G++
Sbjct: 137 ASLENFPIGHL 147


  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
   0.326    0.138    0.426 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,646,180
Number of Sequences: 62578
Number of extensions: 285653
Number of successful extensions: 527
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 527
Number of HSP's gapped (non-prelim): 1
length of query: 283
length of database: 14,973,337
effective HSP length: 98
effective length of query: 185
effective length of database: 8,840,693
effective search space: 1635528205
effective search space used: 1635528205
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)