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= 009013
         (546 letters)

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

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



>pdb|3TEE|A Chain A, Crystal Structure Of Salmonella Flga In Open Form
 pdb|3VKI|A Chain A, Monoclinic Crystal Structure Of Salmonella Flga In Closed
           Form
 pdb|3VKI|B Chain B, Monoclinic Crystal Structure Of Salmonella Flga In Closed
           Form
 pdb|3VKI|C Chain C, Monoclinic Crystal Structure Of Salmonella Flga In Closed
           Form
 pdb|3VKI|D Chain D, Monoclinic Crystal Structure Of Salmonella Flga In Closed
           Form
          Length = 219

 Score = 32.3 bits (72), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 54  LIRLQQNWKVKR-QRVAAPASGNEGFTIDLFDNSLYDSAPVS----RPSSLSTIRIDHDS 108
           L  ++Q W+VK  QRV   A+G EGF+++    ++ ++A       R +S   +    DS
Sbjct: 132 LTMIRQAWRVKAGQRVQVIANG-EGFSVNAEGQAMNNAAVAQNARVRMTSGQIVSGTVDS 190

Query: 109 AGMLAINLPPNS 120
            G + INL PNS
Sbjct: 191 DGNILINLDPNS 202


>pdb|2GMN|A Chain A, Crystal Structure Of Bjp-1, A Subclass B3
           Metallo-beta-lactamase Of Bradyrhizobium Japonicum
 pdb|2GMN|B Chain B, Crystal Structure Of Bjp-1, A Subclass B3
           Metallo-beta-lactamase Of Bradyrhizobium Japonicum
          Length = 274

 Score = 30.4 bits (67), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 9/72 (12%)

Query: 438 QQVASQVIRWLHEEALMVGIKANRDFLSLSFELD----QGETVSL-----VAHVDPEDMR 488
           Q VA +  + L E     G + N D    + ++D    +G+ V+L      AH  P    
Sbjct: 100 QLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSP 159

Query: 489 GCISWWLVMEDG 500
           GC SW + ++DG
Sbjct: 160 GCTSWEMTVKDG 171


>pdb|3LVZ|A Chain A, New Refinement Of The Crystal Structure Of Bjp-1, A
           Subclass B3 Metallo-Beta-Lactamase Of Bradyrhizobium
           Japonicum
 pdb|3LVZ|B Chain B, New Refinement Of The Crystal Structure Of Bjp-1, A
           Subclass B3 Metallo-Beta-Lactamase Of Bradyrhizobium
           Japonicum
 pdb|3M8T|A Chain A, Crystal Structure Of The Complex Between Class B3
           Beta-Lactamase Bjp-1 And 4-Nitrobenzene-Sulfonamide
 pdb|3M8T|B Chain B, Crystal Structure Of The Complex Between Class B3
           Beta-Lactamase Bjp-1 And 4-Nitrobenzene-Sulfonamide
          Length = 294

 Score = 30.0 bits (66), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 9/72 (12%)

Query: 438 QQVASQVIRWLHEEALMVGIKANRDFLSLSFELD----QGETVSL-----VAHVDPEDMR 488
           Q VA +  + L E     G + N D    + ++D    +G+ V+L      AH  P    
Sbjct: 120 QLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSP 179

Query: 489 GCISWWLVMEDG 500
           GC SW + ++DG
Sbjct: 180 GCTSWEMTVKDG 191


>pdb|2INR|A Chain A, Crystal Structure Of A 59 Kda Fragment Of Topoisomerase Iv
           Subunit A (Grla) From Staphylococcus Aureus
          Length = 514

 Score = 28.9 bits (63), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 7/50 (14%)

Query: 33  FKQSAKSLEQQIAK-----EARFYGALIRLQQNWKVKRQRVAAPASGNEG 77
           F++SAK++   I +     ++  Y A++RL Q+WK++   V     GN G
Sbjct: 83  FRKSAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLR--HVLIEMHGNNG 130


  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
   0.317    0.133    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,903,737
Number of Sequences: 62578
Number of extensions: 641541
Number of successful extensions: 1164
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1162
Number of HSP's gapped (non-prelim): 6
length of query: 546
length of database: 14,973,337
effective HSP length: 104
effective length of query: 442
effective length of database: 8,465,225
effective search space: 3741629450
effective search space used: 3741629450
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)