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= 038485
         (184 letters)

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

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



>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
           Binding Of A Tri-Acylated Lipopeptide
          Length = 520

 Score = 30.4 bits (67), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 7/51 (13%)

Query: 51  YLNASLFTPFQQLESLDLTDNKIASCVENEGIERLSRLNNLKMLNLSGNSF 101
           YL+ S+F   Q+LE LDL+ NK+     +  +       NLK L+LS N+F
Sbjct: 59  YLDISVFKFNQELEYLDLSHNKLVKISCHPTV-------NLKHLDLSFNAF 102


>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 = 29.3 bits (64), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 7/66 (10%)

Query: 34  SRVIALDLSDTYGGEYWYLNASLFTPFQQLESLDLTDNKIASCVENEGIERLSRLNNLKM 93
           S V  LDLS    G  + LN+ +F   + L+ L+L  NKI    +    E    L+NL++
Sbjct: 266 SSVRHLDLSH---GFVFSLNSRVFETLKDLKVLNLAYNKINKIAD----EAFYGLDNLQV 318

Query: 94  LNLSGN 99
           LNLS N
Sbjct: 319 LNLSYN 324


>pdb|1P8T|A Chain A, Crystal Structure Of Nogo-66 Receptor
          Length = 285

 Score = 28.5 bits (62), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 52  LNASLFTPFQQLESLDLTDNKIASCVENEGIERLSRLNNLKM 93
           ++A+ FT    LE LDL+DN     V+      L RL+ L +
Sbjct: 70  IDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHL 111


>pdb|1OZN|A Chain A, 1.5a Crystal Structure Of The Nogo Receptor Ligand Binding
           Domain Reveals A Convergent Recognition Scaffold
           Mediating Inhibition Of Myelination
          Length = 285

 Score = 28.5 bits (62), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 52  LNASLFTPFQQLESLDLTDNKIASCVENEGIERLSRLNNLKM 93
           ++A+ FT    LE LDL+DN     V+      L RL+ L +
Sbjct: 71  IDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHL 112


>pdb|3CIG|A Chain A, Crystal Structure Of Mouse Tlr3 Ectodomain
 pdb|3CIY|A Chain A, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
           Double-Stranded Rna
 pdb|3CIY|B Chain B, Mouse Toll-Like Receptor 3 Ectodomain Complexed With
           Double-Stranded Rna
          Length = 697

 Score = 27.3 bits (59), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 52  LNASLFTPFQQLESLDLTDNKIASCVEN--EGIERLSRLN 89
           ++ S F P + L  LDL++N IA+  E+  EG+E L  L+
Sbjct: 471 ISPSPFRPLRNLTILDLSNNNIANINEDLLEGLENLEILD 510


  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
   0.319    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: 4,583,088
Number of Sequences: 62578
Number of extensions: 148187
Number of successful extensions: 334
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 329
Number of HSP's gapped (non-prelim): 21
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
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)