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= 043931
         (161 letters)

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

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



>pdb|3ULS|H Chain H, Crystal Structure Of Fab12
 pdb|3ULS|B Chain B, Crystal Structure Of Fab12
 pdb|3ULU|D Chain D, Structure Of Quaternary Complex Of Human Tlr3ecd With
          Three Fabs (Form1)
 pdb|3ULV|D Chain D, Structure Of Quaternary Complex Of Human Tlr3ecd With
          Three Fabs (Form2)
          Length = 226

 Score = 27.7 bits (60), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 2  ETPSRHLPVLKRMSKLGKKANNFATGVKEHVRLAPKITETVKGKLSL 48
          ++P R L  L  + K  K  NN+A  VK  + + P   +T K + SL
Sbjct: 41 QSPGRGLEWLGIIQKRSKWYNNYAVSVKSRITINP---DTSKNQFSL 84


>pdb|1JG4|A Chain A, Crystal Structure Of L-Isoaspartyl (D-Aspartyl) O-
           Methyltransferase With S-Adenosylmethionine
 pdb|1JG3|A Chain A, Crystal Structure Of L-Isoaspartyl (D-Aspartyl)
           O-Methyltransferase With Adenosine & Vyp(Isp)ha
           Substrate
 pdb|1JG3|B Chain B, Crystal Structure Of L-Isoaspartyl (D-Aspartyl)
           O-Methyltransferase With Adenosine & Vyp(Isp)ha
           Substrate
 pdb|1JG2|A Chain A, Crystal Structure Of L-Isoaspartyl (D-Aspartyl) O-
           Methyltransferase With Adenosine
 pdb|1JG1|A Chain A, Crystal Structure Of L-Isoaspartyl (D-Aspartyl) O-
           Methyltransferase With S-Adenosyl-L-Homocysteine
          Length = 235

 Score = 26.2 bits (56), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 26/42 (61%)

Query: 35  APKITETVKGKLSLGAKIIQVGGVERIFKQLFSVKEGENLLK 76
           APKI E +  +L +G K+I   G   ++++L  V++ ++ +K
Sbjct: 168 APKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIK 209


  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    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,280,512
Number of Sequences: 62578
Number of extensions: 147248
Number of successful extensions: 404
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 403
Number of HSP's gapped (non-prelim): 4
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
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: 47 (22.7 bits)