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= 026084
         (243 letters)

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

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



>pdb|1JI4|A Chain A, Nap Protein From Helicobacter Pylori
 pdb|1JI4|B Chain B, Nap Protein From Helicobacter Pylori
 pdb|1JI4|C Chain C, Nap Protein From Helicobacter Pylori
 pdb|1JI4|D Chain D, Nap Protein From Helicobacter Pylori
 pdb|1JI4|E Chain E, Nap Protein From Helicobacter Pylori
 pdb|1JI4|F Chain F, Nap Protein From Helicobacter Pylori
 pdb|1JI4|G Chain G, Nap Protein From Helicobacter Pylori
 pdb|1JI4|H Chain H, Nap Protein From Helicobacter Pylori
 pdb|1JI4|I Chain I, Nap Protein From Helicobacter Pylori
 pdb|1JI4|J Chain J, Nap Protein From Helicobacter Pylori
 pdb|1JI4|K Chain K, Nap Protein From Helicobacter Pylori
 pdb|1JI4|L Chain L, Nap Protein From Helicobacter Pylori
          Length = 144

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 131 MYAAGFYTYSIFALMFWETRRADFGVSMGHHVATVILIVLSYIFRFARVGSVVLALHDAS 190
           ++ A    Y  FA MF +   A+  V +GHH     L+ LS   +  RV         + 
Sbjct: 36  VHKATEEIYEEFADMFDDL--AERIVQLGHHP----LVTLSEAIKLTRVKEETKTSFHSK 89

Query: 191 DVFLEIGKMSKYIGAE 206
           D+F EI +  KY+  E
Sbjct: 90  DIFKEILEDYKYLEKE 105


>pdb|2VKD|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp-glc And
           Manganese Ion
 pdb|2VKD|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp-glc And
           Manganese Ion
 pdb|2VKD|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp-glc And
           Manganese Ion
 pdb|2VKH|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp-glc And
           Calcium Ion
 pdb|2VKH|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp-glc And
           Calcium Ion
 pdb|2VKH|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp-glc And
           Calcium Ion
 pdb|2VL8|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp,
           Castanospermine And Calcium Ion
 pdb|2VL8|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp,
           Castanospermine And Calcium Ion
 pdb|2VL8|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
           From Clostridium Sordellii In Complex With Udp,
           Castanospermine And Calcium Ion
          Length = 546

 Score = 27.3 bits (59), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 7/55 (12%)

Query: 57  GHHMLDFKTSERKKKIRKFNESAWKCVYFLTAELLALSVTYDEPWFKNTRCFWVG 111
            +++  +K S R K ++KF E       +LT E+L L      P  KN    W+G
Sbjct: 57  DNYLNTYKKSGRNKALKKFKE-------YLTMEVLELKNNSLTPVEKNLHFIWIG 104


  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
   0.329    0.142    0.464 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,456,197
Number of Sequences: 62578
Number of extensions: 283899
Number of successful extensions: 595
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 591
Number of HSP's gapped (non-prelim): 8
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)