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= 0002.0688.p
         (290 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...   480   e-137

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

 Score =  480 bits (1236), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 230/290 (79%), Positives = 257/290 (88%), Gaps = 7/290 (2%)

Query: 1   MKIKFTKMHGAGNDFVVVDAIHQDIALTPAQWKFIADRRFGIGADQMLVVEKTQSEGIDF 60
           MKIKFTKMHGAGNDFVV+DAI+Q I+L+PAQW+FIADRRFGIGADQMLVVEK + EG+DF
Sbjct: 1   MKIKFTKMHGAGNDFVVLDAINQSISLSPAQWQFIADRRFGIGADQMLVVEKARGEGVDF 60

Query: 61  RYRIYNADGGEVEQCGNGARARARAARAFARFVSDKGLTSKRVIRVETMSGIIEPTLEDD 120
           RYRIYNADGGEVEQCGNGARA       F +FV+DKGLTSKR IRVETMSG+IEP LEDD
Sbjct: 61  RYRIYNADGGEVEQCGNGARA-------FVKFVTDKGLTSKRAIRVETMSGVIEPRLEDD 113

Query: 121 GRVTVDMGAPVLSPEQVPFDPSGLDSKAEGDDALWPLDVDGKTRWISVVSMGNPHAVQIV 180
           G++TVDMGAP+L+P  VPFD  GL  + E +D LWPLDV GKT WISVVSMGNPHAVQ+V
Sbjct: 114 GQITVDMGAPILTPADVPFDSHGLQHRNEAEDTLWPLDVAGKTTWISVVSMGNPHAVQVV 173

Query: 181 ADTEAAPVLTDGPLIERHVRFPKRVNAGFMQVVDRHNVNLRVFERGVGETLACGTGACAA 240
            D+EAAPVL++GPLIERH RFPKRVNAGFMQVVDRH+VNLRV+ERG GETLACGTGACAA
Sbjct: 174 EDSEAAPVLSEGPLIERHERFPKRVNAGFMQVVDRHHVNLRVYERGAGETLACGTGACAA 233

Query: 241 VVAGIRRGLLDTPVAVQTHGGELVIRWTGPDKPVMMTGPAVSVFEGEIDI 290
           VVAGIRRGLLD+PVAVQTHGG L I W GP + VMMTGPAVSV+EGEI++
Sbjct: 234 VVAGIRRGLLDSPVAVQTHGGVLNIAWAGPGEAVMMTGPAVSVYEGEIEL 283


  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
   0.321    0.138    0.415 

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: 937,207
Number of extensions: 39498
Number of successful extensions: 126
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 123
Number of HSP's successfully gapped: 1
Length of query: 290
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 206
Effective length of database: 1,222,130
Effective search space: 251758780
Effective search space used: 251758780
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: 130 (54.7 bits)