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= 007128
         (617 letters)

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

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



>pdb|2UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
 pdb|3UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
 pdb|4UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
 pdb|1UAG|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
          Length = 437

 Score = 33.1 bits (74), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 130 CLIPPPSGYKVPIKWPKSRDEVWKANIPHTHLAHEKSDQNWMVVKGEKII 179
           C++       +PI+    R   +  N+   HL H++  + W+ VKGEK++
Sbjct: 208 CVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQG-ETWLRVKGEKVL 256


>pdb|2JFF|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
           Containing Sulfonamide Inhibitor
 pdb|2JFG|A Chain A, Crystal Structure Of Murd Ligase In Complex With Uma And
           Adp
 pdb|2JFH|A Chain A, Crystal Structure Of Murd Ligase In Complex With L-Glu
           Containing Sulfonamide Inhibitor
 pdb|2UUO|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
           Containing Sulfonamide Inhibitor
 pdb|2UUP|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
           Containing Sulfonamide Inhibitor
 pdb|2VTD|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
           Containing Sulfonamide Inhibitor
 pdb|2VTE|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
           Containing Sulfonamide Inhibitor
 pdb|2Y68|A Chain A, Structure-Based Design Of A New Series Of D-Glutamic Acid-
           Based Inhibitors Of Bacterial Murd Ligase
 pdb|2Y66|A Chain A, New 5-Benzylidenethiazolidine-4-One Inhibitors Of
           Bacterial Murd Ligase: Design, Synthesis, Crystal
           Structures, And Biological Evaluation
 pdb|2Y67|A Chain A, New 5-Benzylidenethiazolidine-4-One Inhibitors Of
           Bacterial Murd Ligase: Design, Synthesis, Crystal
           Structures, And Biological Evaluation
 pdb|2Y1O|A Chain A, Dual-target Inhibitor Of Murd And Mure Ligases: Design,
           Synthesis And Binding Mode Studies
          Length = 445

 Score = 33.1 bits (74), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 130 CLIPPPSGYKVPIKWPKSRDEVWKANIPHTHLAHEKSDQNWMVVKGEKII 179
           C++       +PI+    R   +  N+   HL H++  + W+ VKGEK++
Sbjct: 209 CVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQG-ETWLRVKGEKVL 257


>pdb|2WJP|A Chain A, Crystal Structure Of Murd Ligase In Complex With D-Glu
           Containing Rhodanine Inhibitor
 pdb|2X5O|A Chain A, Discovery Of Novel 5-Benzylidenerhodanine- And
           5-Benzylidene- Thiazolidine-2,4-Dione Inhibitors Of Murd
           Ligase
 pdb|2XPC|A Chain A, Second-Generation Sulfonamide Inhibitors Of Murd: Activity
           Optimisation With Conformationally Rigid Analogues Of D-
           Glutamic Acid
          Length = 439

 Score = 33.1 bits (74), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 130 CLIPPPSGYKVPIKWPKSRDEVWKANIPHTHLAHEKSDQNWMVVKGEKII 179
           C++       +PI+    R   +  N+   HL H++  + W+ VKGEK++
Sbjct: 208 CVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQG-ETWLRVKGEKVL 256


>pdb|1E0D|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
 pdb|1EEH|A Chain A, Udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate Ligase
          Length = 437

 Score = 33.1 bits (74), Expect = 0.48,   Method: Compositional matrix adjust.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 130 CLIPPPSGYKVPIKWPKSRDEVWKANIPHTHLAHEKSDQNWMVVKGEKII 179
           C++       +PI+    R   +  N+   HL H++  + W+ VKGEK++
Sbjct: 208 CVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQG-ETWLRVKGEKVL 256


  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    0.137    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,981,227
Number of Sequences: 62578
Number of extensions: 886572
Number of successful extensions: 1630
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1630
Number of HSP's gapped (non-prelim): 5
length of query: 617
length of database: 14,973,337
effective HSP length: 105
effective length of query: 512
effective length of database: 8,402,647
effective search space: 4302155264
effective search space used: 4302155264
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)