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= 007425
         (604 letters)

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

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



>pdb|3R38|A Chain A, 2.23 Angstrom Resolution Crystal Structure Of
           Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase (Mura)
           From Listeria Monocytogenes Egd-E
          Length = 454

 Score = 30.0 bits (66), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 29/128 (22%), Positives = 54/128 (42%), Gaps = 15/128 (11%)

Query: 202 LLNATLVVPKFMYSSVWRDVSQFSDIYQEEHFINYLTPDIRMVKELPNKLQSLDLEAIGS 261
           ++ ATL+  K   +SV ++V   SD++     + YL  D+  V +       + ++A G 
Sbjct: 52  VIAATLLASK--GTSVLKNVPNLSDVFTINEVLKYLNADVSFVND------EVTVDATGE 103

Query: 262 VVTDVDIPKESKPSFYLKNIIPILLRNGVVHL-LGFGNRLAFDPIPFQLQRLRCRCNFHA 320
           + +D       K    +  + P+L R G   + L  G  +   P+   L+       F A
Sbjct: 104 ITSDAPFEYVRKMRASIVVMGPLLARTGSARVALPGGCAIGSRPVDLHLK------GFEA 157

Query: 321 LQFAPKIQ 328
           +    KI+
Sbjct: 158 MGAVVKIE 165


  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
   0.323    0.137    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,844,063
Number of Sequences: 62578
Number of extensions: 597900
Number of successful extensions: 1018
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1018
Number of HSP's gapped (non-prelim): 2
length of query: 604
length of database: 14,973,337
effective HSP length: 104
effective length of query: 500
effective length of database: 8,465,225
effective search space: 4232612500
effective search space used: 4232612500
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)