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= 0027.0044.p
         (119 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313578|ref|YP_003777670.1| diaminopimelate epimerase [Herb...   211   2e-56

>gi|300313578|ref|YP_003777670.1| diaminopimelate epimerase
           [Herbaspirillum seropedicae SmR1]
          Length = 287

 Score =  211 bits (536), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 99/106 (93%), Positives = 102/106 (96%)

Query: 10  PADVPFDSRGLQHRTEAEDTLWPLDVAGKTTWISVVSMGNPHAVQVVEDSEAAPVLVDGP 69
           PADVPFDS GLQHR EAEDTLWPLDVAGKTTWISVVSMGNPHAVQVVEDSEAAPVL +GP
Sbjct: 127 PADVPFDSHGLQHRNEAEDTLWPLDVAGKTTWISVVSMGNPHAVQVVEDSEAAPVLSEGP 186

Query: 70  LIEHHERFPRRVNAGFMQVVDRHHINLRVYERGAGETLACGTGACA 115
           LIE HERFP+RVNAGFMQVVDRHH+NLRVYERGAGETLACGTGACA
Sbjct: 187 LIERHERFPKRVNAGFMQVVDRHHVNLRVYERGAGETLACGTGACA 232


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.320    0.135    0.436 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 420,098
Number of extensions: 16176
Number of successful extensions: 40
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 40
Number of HSP's successfully gapped: 1
Length of query: 119
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 45
Effective length of database: 1,269,480
Effective search space: 57126600
Effective search space used: 57126600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 124 (52.4 bits)