BLASTP 2.2.18 [Mar-02-2008]


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= 0583.0002.p
         (285 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

lin0128 [M] COG5632 N-acetylmuramoyl-L-alanine amidase                127   2e-29

>lin0128 [M] COG5632 N-acetylmuramoyl-L-alanine amidase
          Length = 289

 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 62/142 (43%), Positives = 87/142 (61%), Gaps = 9/142 (6%)

Query: 2   LTLEQVKAKSAKRLD--GLQPVVKAAATALIERCYAREVNIVITQGLRTIAEQDALYAQG 59
           LT   +  K+ ++L+  G+  +       +I++     + + + QG R+ AEQ+ALYAQG
Sbjct: 3   LTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQG 62

Query: 60  RTKPGQIVTNAKGGHSYHNYGLAIDFALLLPDGRNVSWDMNRDGDGDKVADWNEVVQEAK 119
           RTKPG IVTNAKGG S HNYG+A+D  L   DG++V W+          + W +VV   K
Sbjct: 63  RTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWE-------STTSRWKKVVAAMK 115

Query: 120 ALGFEWGGDWTSIKDYPHFQMS 141
           A GF+WGGDW S KDYPHF++ 
Sbjct: 116 AEGFKWGGDWKSFKDYPHFELC 137


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.315    0.131    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 20,437,991
Number of extensions: 852340
Number of successful extensions: 3039
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 3039
Number of HSP's successfully gapped: 1
Length of query: 285
Length of database: 38,378,431
Length adjustment: 105
Effective length of query: 180
Effective length of database: 26,268,361
Effective search space: 4728304980
Effective search space used: 4728304980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 115 (48.9 bits)