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= 0002.0065.p
         (58 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309742|ref|YP_003773834.1| shikimate 5-dehydrogenase [Herb...    89   8e-20

>gi|300309742|ref|YP_003773834.1| shikimate 5-dehydrogenase
           [Herbaspirillum seropedicae SmR1]
          Length = 271

 Score = 88.6 bits (218), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 43/58 (74%), Positives = 48/58 (82%)

Query: 1   MYGKQPTVFMEFAHRHGAVTRDGLGMLVEQAAEAFLLWRGVRPETAGVFTALRRQLSQ 58
           MYG+ PTVFM+ A +HGA  RDGLGMLVEQAAEAF  WRGVRP TA VF +LR+QLSQ
Sbjct: 214 MYGRGPTVFMQSAQQHGAHVRDGLGMLVEQAAEAFQWWRGVRPATAEVFASLRQQLSQ 271


  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
   0.326    0.137    0.417 

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: 181,631
Number of extensions: 5150
Number of successful extensions: 22
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 22
Number of HSP's successfully gapped: 1
Length of query: 58
Length of database: 1,619,870
Length adjustment: 31
Effective length of query: 27
Effective length of database: 1,473,085
Effective search space: 39773295
Effective search space used: 39773295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 123 (52.0 bits)