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= 035891
         (309 letters)

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

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



>pdb|3VQ1|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
 pdb|3VQ1|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LIPID IVA COMPLEX
 pdb|3VQ2|A Chain A, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
 pdb|3VQ2|B Chain B, Crystal Structure Of Mouse Tlr4MD-2LPS COMPLEX
          Length = 606

 Score = 30.8 bits (68), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 10/96 (10%)

Query: 72  TITLQSFAALHRLLTSPSLQSIFSNTPSLCLRNCHSLSSLSVFTLASLRHLE-----ALD 126
           T+T+   +   + +  PSL  +  +  +L    C S S L      SLRHL+     A+ 
Sbjct: 334 TLTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGT---NSLRHLDLSFNGAII 390

Query: 127 MT-NCKDLEEME-IDYAGEEVKRIRETHGFFSLHKV 160
           M+ N   LEE++ +D+    +KR+ E   F SL K+
Sbjct: 391 MSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKL 426


>pdb|2Z64|A Chain A, Crystal Structure Of Mouse Tlr4 And Mouse Md-2 Complex
          Length = 599

 Score = 30.8 bits (68), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 10/96 (10%)

Query: 72  TITLQSFAALHRLLTSPSLQSIFSNTPSLCLRNCHSLSSLSVFTLASLRHLE-----ALD 126
           T+T+   +   + +  PSL  +  +  +L    C S S L      SLRHL+     A+ 
Sbjct: 329 TLTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGT---NSLRHLDLSFNGAII 385

Query: 127 MT-NCKDLEEME-IDYAGEEVKRIRETHGFFSLHKV 160
           M+ N   LEE++ +D+    +KR+ E   F SL K+
Sbjct: 386 MSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKL 421


>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
           Iii Effector Xcv3220 (Xopl)
          Length = 328

 Score = 29.6 bits (65), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 194 ISLEKLGEVPSEEMQNLFPFARLESLSLYALGNLRSIYPKALPFPHLKELEVNLCPKLEK 253
           I    L E+P    Q    FA LE+L+L A   LR++         L+EL +  CP+L +
Sbjct: 111 IDAAGLXELPDTXQQ----FAGLETLTL-ARNPLRALPASIASLNRLRELSIRACPELTE 165

Query: 254 LP 255
           LP
Sbjct: 166 LP 167


  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
   0.322    0.136    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,280,002
Number of Sequences: 62578
Number of extensions: 315199
Number of successful extensions: 694
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 692
Number of HSP's gapped (non-prelim): 5
length of query: 309
length of database: 14,973,337
effective HSP length: 99
effective length of query: 210
effective length of database: 8,778,115
effective search space: 1843404150
effective search space used: 1843404150
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)