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= 003790
         (795 letters)

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

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



>pdb|1BYR|A Chain A, Crystal Structure Of A Phospholipase D Family Member, Nuc
           From Salmonella Typhimurium
 pdb|1BYS|A Chain A, Crystal Structure Of Nuc Complexed With Tungstate
          Length = 155

 Score = 33.9 bits (76), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 41/86 (47%), Gaps = 12/86 (13%)

Query: 505 EGMPRASSLSSIDSIMTPSRM---SGGDPDTTCSSTHASTEPSEYVRGLDPK---SKRLS 558
           EG  R   LS+IDS  T  RM   S   PD   +   A        RG+D K    +R +
Sbjct: 12  EGSARVLVLSAIDSAKTSIRMMAYSFTAPDIMKALVAAKK------RGVDVKIVIDERGN 65

Query: 559 SGRSNVMAEPEVIHPQLPLSTTPNWP 584
           +GR+++ A   + +  +PL T  N+P
Sbjct: 66  TGRASIAAMNYIANSGIPLRTDSNFP 91


>pdb|1VCL|A Chain A, Crystal Structure Of Hemolytic Lectin Cel-iii
 pdb|1VCL|B Chain B, Crystal Structure Of Hemolytic Lectin Cel-iii
 pdb|2Z48|A Chain A, Crystal Structure Of Hemolytic Lectin Cel-Iii Complexed
           With Galnac
 pdb|2Z48|B Chain B, Crystal Structure Of Hemolytic Lectin Cel-Iii Complexed
           With Galnac
 pdb|2Z49|A Chain A, Crystal Structure Of Hemolytic Lectin Cel-Iii Complexed
           With Methyl-Alpha-D-Galactopylanoside
 pdb|2Z49|B Chain B, Crystal Structure Of Hemolytic Lectin Cel-Iii Complexed
           With Methyl-Alpha-D-Galactopylanoside
          Length = 432

 Score = 31.2 bits (69), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 2/36 (5%)

Query: 559 SGRSNVMAEPEVIHPQLPLSTTPNWPRTRSKSRTDK 594
           SG +NVM+ P  ++P++P  ++  W + R K+ TD 
Sbjct: 68  SGNANVMSSPCTLYPEIP--SSQRWRQGRRKTFTDN 101


  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
   0.315    0.132    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,345,793
Number of Sequences: 62578
Number of extensions: 880724
Number of successful extensions: 2027
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2027
Number of HSP's gapped (non-prelim): 4
length of query: 795
length of database: 14,973,337
effective HSP length: 107
effective length of query: 688
effective length of database: 8,277,491
effective search space: 5694913808
effective search space used: 5694913808
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)