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= 0001.0072.p
         (115 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310399|ref|YP_003774491.1| D-ribulose/ribitol kinase [Herb...   134   1e-33

>gi|300310399|ref|YP_003774491.1| D-ribulose/ribitol kinase
           [Herbaspirillum seropedicae SmR1]
          Length = 548

 Score =  134 bits (338), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 66/87 (75%), Positives = 74/87 (85%)

Query: 28  HRLGPDXGGGGARAGVFDRSGKLCGSAKHDIDLFRDERRARVEQSSAQIWDAVCHAVRGA 87
           + +G D G G ARAGVFD  G+L  SA+HDIDLFRDERRARVEQSSAQIW+AVC AVR A
Sbjct: 4   YLIGIDVGTGSARAGVFDPQGQLLASARHDIDLFRDERRARVEQSSAQIWEAVCQAVRAA 63

Query: 88  IAKAGIDPASVTGIGVDATCSLVVQGA 114
           + K+GIDPA+V GIGVDATCSLVVQGA
Sbjct: 64  VTKSGIDPAAVAGIGVDATCSLVVQGA 90


  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    0.137    0.434 

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: 344,033
Number of extensions: 11119
Number of successful extensions: 43
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 43
Number of HSP's successfully gapped: 1
Length of query: 115
Length of database: 1,619,870
Length adjustment: 73
Effective length of query: 42
Effective length of database: 1,274,215
Effective search space: 53517030
Effective search space used: 53517030
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)