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= psy10689
         (369 letters)

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

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



>pdb|3T24|A Chain A, Crystal Structure Of Pseudomonas Aeruginosa Opdq
 pdb|3T24|B Chain B, Crystal Structure Of Pseudomonas Aeruginosa Opdq
 pdb|3T24|C Chain C, Crystal Structure Of Pseudomonas Aeruginosa Opdq
          Length = 401

 Score = 29.3 bits (64), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 231 KRKSTVGWSIGNVLLDFAGGLFSLLQMLILAYNFGKCKTLDSYWDQIHLSLIKT 284
           KR+  V   + +   DFAGG +     L  +Y++GK   LD+++ Q +L L+ T
Sbjct: 178 KRQIVVRSGLTSDKFDFAGGSYKWTDNLSTSYHYGK---LDNFYKQHYLGLVHT 228


>pdb|2DDY|A Chain A, Solution Structure Of Matrilysin (Mmp-7) Complexed To
           Constraint Conformational Sulfonamide Inhibitor
          Length = 173

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 80  GASAHCQVLVNWQRKSVIGLNFDYLGLNMIGHSL----YGVYNFVLYFSY 125
           G  AH      W   S +G+NF Y   + +GHSL        N V+Y +Y
Sbjct: 93  GGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTY 142


>pdb|2Y6D|A Chain A, The Discovery Of Mmp7 Inhibitors Exploiting A Novel
           Selectivity Trigger
          Length = 174

 Score = 28.9 bits (63), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 80  GASAHCQVLVNWQRKSVIGLNFDYLGLNMIGHSL----YGVYNFVLYFSY 125
           G  AH      W   S +G+NF Y   + +GHSL        N V+Y +Y
Sbjct: 94  GGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTY 143


>pdb|2Y6C|A Chain A, The Discovery Of Mmp7 Inhibitors Exploiting A Novel
           Selectivity Trigger
          Length = 165

 Score = 28.9 bits (63), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 17/34 (50%)

Query: 80  GASAHCQVLVNWQRKSVIGLNFDYLGLNMIGHSL 113
           G  AH      W   S +G+NF Y   + +GHSL
Sbjct: 94  GGDAHFDEDERWTDGSSLGINFLYAATHELGHSL 127


>pdb|1MMP|A Chain A, Matrilysin Complexed With Carboxylate Inhibitor
 pdb|1MMP|B Chain B, Matrilysin Complexed With Carboxylate Inhibitor
 pdb|1MMQ|A Chain A, Matrilysin Complexed With Hydroxamate Inhibitor
 pdb|1MMR|A Chain A, Matrilysin Complexed With Sulfodiimine Inhibitor
          Length = 170

 Score = 28.9 bits (63), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 80  GASAHCQVLVNWQRKSVIGLNFDYLGLNMIGHSL----YGVYNFVLYFSY 125
           G  AH      W   S +G+NF Y   + +GHSL        N V+Y +Y
Sbjct: 93  GGDAHFDEDERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTY 142


  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    0.140    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,846,782
Number of Sequences: 62578
Number of extensions: 420199
Number of successful extensions: 827
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 822
Number of HSP's gapped (non-prelim): 6
length of query: 369
length of database: 14,973,337
effective HSP length: 100
effective length of query: 269
effective length of database: 8,715,537
effective search space: 2344479453
effective search space used: 2344479453
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: 52 (24.6 bits)