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= 045917
         (162 letters)

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

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



>pdb|4FR5|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Y210s
           Mutant From Helicobacter Pylori In Complex With
           Shikimate
 pdb|4FR5|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Y210s
           Mutant From Helicobacter Pylori In Complex With
           Shikimate
          Length = 271

 Score = 26.9 bits (58), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 89  EMLKTGLRPDNLTYPFVVKASDQCLLI-GVG---GSVHSLIFKVGLHSDKYIG-NT-LLR 142
           E L  GL   N+T PF  +A   C  I G+    G+V++L+    L +D+ +G NT  L 
Sbjct: 53  EFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLV----LENDELVGYNTDALG 108

Query: 143 MYAACKEIDFAKAL 156
            Y + K+ ++  AL
Sbjct: 109 FYLSLKQKNYQNAL 122


>pdb|4FPX|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Q237n
           Mutant From Helicobacter Pylori
 pdb|4FPX|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Q237n
           Mutant From Helicobacter Pylori
          Length = 271

 Score = 26.9 bits (58), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 89  EMLKTGLRPDNLTYPFVVKASDQCLLI-GVG---GSVHSLIFKVGLHSDKYIG-NT-LLR 142
           E L  GL   N+T PF  +A   C  I G+    G+V++L+    L +D+ +G NT  L 
Sbjct: 53  EFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLV----LENDELVGYNTDALG 108

Query: 143 MYAACKEIDFAKAL 156
            Y + K+ ++  AL
Sbjct: 109 FYLSLKQKNYQNAL 122


>pdb|4FQ8|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Y210a
           Mutant From Helicobacter Pylori In Complex With
           Shikimate
 pdb|4FQ8|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Y210a
           Mutant From Helicobacter Pylori In Complex With
           Shikimate
          Length = 271

 Score = 26.9 bits (58), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 89  EMLKTGLRPDNLTYPFVVKASDQCLLI-GVG---GSVHSLIFKVGLHSDKYIG-NT-LLR 142
           E L  GL   N+T PF  +A   C  I G+    G+V++L+    L +D+ +G NT  L 
Sbjct: 53  EFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLV----LENDELVGYNTDALG 108

Query: 143 MYAACKEIDFAKAL 156
            Y + K+ ++  AL
Sbjct: 109 FYLSLKQKNYQNAL 122


>pdb|3PHG|A Chain A, Crystal Structure Of The Shikimate 5-Dehydrogenase (Aroe)
           From Helicobacter Pylori
 pdb|3PHG|B Chain B, Crystal Structure Of The Shikimate 5-Dehydrogenase (Aroe)
           From Helicobacter Pylori
 pdb|3PHH|A Chain A, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori
           In Complex With Shikimate
 pdb|3PHI|A Chain A, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori
           In Complex With Shikimate And Nadph
 pdb|3PHI|B Chain B, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori
           In Complex With Shikimate And Nadph
 pdb|3PHJ|A Chain A, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori
           In Complex With 3-Dehydroshikimate
 pdb|3PHJ|B Chain B, Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori
           In Complex With 3-Dehydroshikimate
          Length = 269

 Score = 26.9 bits (58), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 89  EMLKTGLRPDNLTYPFVVKASDQCLLI-GVG---GSVHSLIFKVGLHSDKYIG-NT-LLR 142
           E L  GL   N+T PF  +A   C  I G+    G+V++L+    L +D+ +G NT  L 
Sbjct: 53  EFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLV----LENDELVGYNTDALG 108

Query: 143 MYAACKEIDFAKAL 156
            Y + K+ ++  AL
Sbjct: 109 FYLSLKQKNYQNAL 122


>pdb|3LXU|X Chain X, Crystal Structure Of Tripeptidyl Peptidase 2 (Tpp Ii)
          Length = 1354

 Score = 26.9 bits (58), Expect = 5.3,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 22/43 (51%)

Query: 68   NTLIRAYAKTSCSIESIKLFDEMLKTGLRPDNLTYPFVVKASD 110
            NTLI A +K   ++  + + D+ +K  L   N  Y  ++K  D
Sbjct: 1238 NTLIEALSKKGIAVAKLAVLDDCIKDSLAEINELYTEIIKFVD 1280


>pdb|4FOS|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Q237a
           Mutant From Helicobacter Pylori In Complex With
           Shikimate
          Length = 271

 Score = 26.9 bits (58), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 89  EMLKTGLRPDNLTYPFVVKASDQCLLI-GVG---GSVHSLIFKVGLHSDKYIG-NT-LLR 142
           E L  GL   N+T PF  +A   C  I G+    G+V++L+    L +D+ +G NT  L 
Sbjct: 53  EFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLV----LENDELVGYNTDALG 108

Query: 143 MYAACKEIDFAKAL 156
            Y + K+ ++  AL
Sbjct: 109 FYLSLKQKNYQNAL 122


>pdb|4FOO|A Chain A, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Q237k
           Mutant From Helicobacter Pylori
 pdb|4FOO|B Chain B, Crystal Structure Of Shikimate Dehydrogenase (Aroe) Q237k
           Mutant From Helicobacter Pylori
          Length = 271

 Score = 26.9 bits (58), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)

Query: 89  EMLKTGLRPDNLTYPFVVKASDQCLLI-GVG---GSVHSLIFKVGLHSDKYIG-NT-LLR 142
           E L  GL   N+T PF  +A   C  I G+    G+V++L+    L +D+ +G NT  L 
Sbjct: 53  EFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLV----LENDELVGYNTDALG 108

Query: 143 MYAACKEIDFAKAL 156
            Y + K+ ++  AL
Sbjct: 109 FYLSLKQKNYQNAL 122


  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
   0.326    0.139    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,478,080
Number of Sequences: 62578
Number of extensions: 181130
Number of successful extensions: 1133
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1132
Number of HSP's gapped (non-prelim): 10
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)