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= 004019
         (779 letters)

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

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



>pdb|3CEI|A Chain A, Crystal Structure Of Superoxide Dismutase From
           Helicobacter Pylori
 pdb|3CEI|B Chain B, Crystal Structure Of Superoxide Dismutase From
           Helicobacter Pylori
          Length = 213

 Score = 30.4 bits (67), Expect = 3.8,   Method: Composition-based stats.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 8/98 (8%)

Query: 349 CLSSSKAFLS--VKNQLEKSKSEVFKYQALFEKLQVEKDNLAWRETELNMKIDLVDVFRR 406
           CLS     LS  +K  LEK    + K++  F K         W     N+    +++ + 
Sbjct: 79  CLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQT 138

Query: 407 SSA---VTDSKIADLGIEIQKQ---IDEKNRIEMRLEE 438
           S+A   VTD K+  L +++ +    ID KN   + LE+
Sbjct: 139 SNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEK 176


>pdb|2V0X|A Chain A, The Dimerization Domain Of Lap2alpha
 pdb|2V0X|B Chain B, The Dimerization Domain Of Lap2alpha
          Length = 235

 Score = 30.0 bits (66), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 12/75 (16%)

Query: 78  YDSTLKVVNKSWEELITDLESCSMRARESSNGQESRCLSIIEDVTPHPSHD----AFLSR 133
           ++S LKVV + W+++   L S + R   SS  + +R LS+       P  D     F+S 
Sbjct: 36  HESILKVVEEEWQQIDRQLPSVACRYPVSSI-EAARILSV-------PKVDDEILGFISE 87

Query: 134 LMETGATESSSADNC 148
                AT++SS ++C
Sbjct: 88  ATPAAATQASSTESC 102


>pdb|2BVM|A Chain A, Crystal Structure Of The Catalytic Domain Of Toxin B From
           Clostridium Difficile In Complex With Udp, Glc And
           Manganese Ion
          Length = 542

 Score = 29.6 bits (65), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 4/53 (7%)

Query: 458 SFPEDMSAMQRQLSKYKEAALDIHILRADV----LSLTNVLERKVKECETLLA 506
           S PE  +A  + L  +KE +++IH++ AD+    +S TN+ +   +E  +L +
Sbjct: 469 SGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWS 521


>pdb|2BVL|A Chain A, Crystal Structure Of The Catalytic Domain Of Toxin B From
           Clostridium Difficile In Complex With Udp, Glc And
           Manganese Ion
          Length = 543

 Score = 29.3 bits (64), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 4/53 (7%)

Query: 458 SFPEDMSAMQRQLSKYKEAALDIHILRADV----LSLTNVLERKVKECETLLA 506
           S PE  +A  + L  +KE +++IH++ AD+    +S TN+ +   +E  +L +
Sbjct: 469 SGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWS 521


  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
   0.313    0.127    0.336 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,482,881
Number of Sequences: 62578
Number of extensions: 670839
Number of successful extensions: 1919
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 1892
Number of HSP's gapped (non-prelim): 47
length of query: 779
length of database: 14,973,337
effective HSP length: 106
effective length of query: 673
effective length of database: 8,340,069
effective search space: 5612866437
effective search space used: 5612866437
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)