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= 030311
         (179 letters)

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

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



>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
           Ra Complex
 pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
           Ra Complex
          Length = 605

 Score = 28.1 bits (61), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 63  VAAPGLSESDFRCAVESTLFKQWLKN 88
           +A   L+++DF C  E   F QW+K+
Sbjct: 545 LAFLNLTQNDFACTCEHQSFLQWIKD 570


>pdb|2YVM|A Chain A, Crystal Structure Of Ndx2 In Complex With Mg2+ From
           Thermus Thermophilus Hb8
 pdb|2YVN|A Chain A, Crystal Structure Of Ndx2 From Thermus Thermophilus Hb8
 pdb|2YVO|A Chain A, Crystal Structure Of Ndx2 In Complex With Mg2+ And Amp
           From Thermus Thermophilus Hb8
 pdb|2YVP|A Chain A, Crystal Structure Of Ndx2 In Complex With Mg2+ And Ampcpr
           From Thermus Thermophilus Hb8
          Length = 182

 Score = 27.7 bits (60), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 18/23 (78%)

Query: 134 QKVRVPTGRVILELPAGMLDDDK 156
           ++ R PTG+ +LE+PAG +D+ +
Sbjct: 59  RQYRHPTGKFLLEVPAGKVDEGE 81


>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 = 27.7 bits (60), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 63  VAAPGLSESDFRCAVESTLFKQWLKN 88
           +A   L+++DF C  E   F QW+K+
Sbjct: 569 LAFLNLTQNDFACTCEHQSFLQWIKD 594


>pdb|2Z66|A Chain A, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
           Hagfish Vlrb.61
 pdb|2Z66|B Chain B, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
           Hagfish Vlrb.61
 pdb|2Z66|C Chain C, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
           Hagfish Vlrb.61
 pdb|2Z66|D Chain D, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
           Hagfish Vlrb.61
          Length = 306

 Score = 27.7 bits (60), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 63  VAAPGLSESDFRCAVESTLFKQWLKN 88
           +A   L+++DF C  E   F QW+K+
Sbjct: 250 LAFLNLTQNDFACTCEHQSFLQWIKD 275


>pdb|2RRL|A Chain A, Solution Structure Of The C-Terminal Domain Of The Flik
          Length = 169

 Score = 26.9 bits (58), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 3/40 (7%)

Query: 33 VCSKMPTESSPSPLTHSITIP---SQLSQPVHVVAAPGLS 69
            +K+  +S P+P+TH   +P   S  +QP+ V +AP LS
Sbjct: 23 TSAKVEVDSPPAPVTHGAAMPTLSSATAQPLPVASAPVLS 62


  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
   0.320    0.136    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,766,923
Number of Sequences: 62578
Number of extensions: 178514
Number of successful extensions: 341
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 339
Number of HSP's gapped (non-prelim): 5
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)