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= psy2168
         (516 letters)

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

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



>pdb|2Z23|A Chain A, Crystal Structure Of Y.Pestis Oligo Peptide Binding
           Protein Oppa With Tri-Lysine Ligand
          Length = 517

 Score = 35.8 bits (81), Expect = 0.058,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 29/45 (64%)

Query: 51  IITDSIKQTEIFKSSTFGQLIFQCHEVRNQLERLQCFQQVQIEID 95
           ++++S   T  +KSS F +LI    +V+++ ER   +QQ +I++D
Sbjct: 430 MLSNSSNNTTHYKSSVFDKLIEDTLKVKSEKERADLYQQAEIQLD 474


>pdb|2X3L|A Chain A, Crystal Structure Of The Orn_lys_arg Decarboxylase Family
           Protein Sar0482 From Methicillin-Resistant
           Staphylococcus Aureus
 pdb|2X3L|B Chain B, Crystal Structure Of The Orn_lys_arg Decarboxylase Family
           Protein Sar0482 From Methicillin-Resistant
           Staphylococcus Aureus
          Length = 446

 Score = 30.0 bits (66), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 55/135 (40%), Gaps = 12/135 (8%)

Query: 23  DAMLGHVMVAPARVDRVKVEGIGRTY--DDIITDSIKQTEIFKSSTFGQLIFQCHEVRNQ 80
           +  +GH+      +D+ ++ G+   +  +++I  S+KQ E  K S +             
Sbjct: 28  NMTIGHLSQLSMTMDKTEIPGLDDLHHPEEVILKSMKQVE--KHSDYDGYFLVNGTTSGI 85

Query: 81  LERLQCFQQVQIEIDASKGP--------DATPEHGYEITFRVKELKRYRAGVTTSIGNNE 132
           L  +Q F Q + +I  ++          D + + G+ I      L  +   V  S  NN+
Sbjct: 86  LSVIQSFSQKKGDILMARNVHKSVLHALDISQQEGHFIETHQSPLTNHYNKVNLSRLNND 145

Query: 133 GSVVVWGKMPNLYGR 147
           G  +V    PN YG 
Sbjct: 146 GHKLVVLTYPNYYGE 160


>pdb|3O6X|A Chain A, Crystal Structure Of The Type Iii Glutamine Synthetase
           From Bacteroides Fragilis
 pdb|3O6X|B Chain B, Crystal Structure Of The Type Iii Glutamine Synthetase
           From Bacteroides Fragilis
 pdb|3O6X|C Chain C, Crystal Structure Of The Type Iii Glutamine Synthetase
           From Bacteroides Fragilis
 pdb|3O6X|D Chain D, Crystal Structure Of The Type Iii Glutamine Synthetase
           From Bacteroides Fragilis
 pdb|3O6X|E Chain E, Crystal Structure Of The Type Iii Glutamine Synthetase
           From Bacteroides Fragilis
 pdb|3O6X|F Chain F, Crystal Structure Of The Type Iii Glutamine Synthetase
           From Bacteroides Fragilis
          Length = 729

 Score = 28.5 bits (62), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 25/39 (64%), Gaps = 1/39 (2%)

Query: 187 QVNEMPASSCKLLEQGLILDYAILFPTIKNSIEWNGLIR 225
           Q+NE  AS  KL+E+G+  D AI F  +K +I  + LIR
Sbjct: 496 QLNEFKASVDKLMEEGIGKDEAI-FRILKENIIASELIR 533


  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
   0.320    0.138    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,340,313
Number of Sequences: 62578
Number of extensions: 631822
Number of successful extensions: 1298
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1295
Number of HSP's gapped (non-prelim): 6
length of query: 516
length of database: 14,973,337
effective HSP length: 103
effective length of query: 413
effective length of database: 8,527,803
effective search space: 3521982639
effective search space used: 3521982639
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)