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= 0241.0055.p
         (171 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...   246   7e-67

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

 Score =  246 bits (628), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 116/142 (81%), Positives = 128/142 (90%)

Query: 2   IRVETMSGVIEPTLEDDGRVTVDMGAPVLTPEQVPFDPSGLNSKIEGDDALWPLDVNGKT 61
           IRVETMSGVIEP LEDDG++TVDMGAP+LTP  VPFD  GL  + E +D LWPLDV GKT
Sbjct: 97  IRVETMSGVIEPRLEDDGQITVDMGAPILTPADVPFDSHGLQHRNEAEDTLWPLDVAGKT 156

Query: 62  SWISVVSMGNPHAVQIVADTEAAPVLTDGPLIERHPRFPKRVNAGFMQVVDRHNVNLRVF 121
           +WISVVSMGNPHAVQ+V D+EAAPVL++GPLIERH RFPKRVNAGFMQVVDRH+VNLRV+
Sbjct: 157 TWISVVSMGNPHAVQVVEDSEAAPVLSEGPLIERHERFPKRVNAGFMQVVDRHHVNLRVY 216

Query: 122 ERGVGETLACGTGACAAVVAGI 143
           ERG GETLACGTGACAAVVAGI
Sbjct: 217 ERGAGETLACGTGACAAVVAGI 238


  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
   0.318    0.136    0.413 

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: 557,049
Number of extensions: 22579
Number of successful extensions: 64
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 64
Number of HSP's successfully gapped: 1
Length of query: 171
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 92
Effective length of database: 1,245,805
Effective search space: 114614060
Effective search space used: 114614060
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 (21.7 bits)
S2: 127 (53.5 bits)