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= 0131.0004.p
         (64 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312102|ref|YP_003776194.1| LysR family transcription regul...   100   3e-23

>gi|300312102|ref|YP_003776194.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 305

 Score =  100 bits (249), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/63 (80%), Positives = 56/63 (88%)

Query: 1   VRLGASTGAIAHLLPQALEVLGQDHPGIDVQVEVLTSQDTLARLSEGTLDVGLVALPQTP 60
           VRLGASTGAIA+LLPQALE LG+ HPGIDVQV VLTSQ+TLARL+ G LD+GLVALPQ P
Sbjct: 96  VRLGASTGAIAYLLPQALEQLGRSHPGIDVQVMVLTSQETLARLAAGALDIGLVALPQAP 155

Query: 61  VAN 63
           VA 
Sbjct: 156 VAG 158


  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
   0.315    0.134    0.372 

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: 217,053
Number of extensions: 7216
Number of successful extensions: 57
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 57
Number of HSP's successfully gapped: 1
Length of query: 64
Length of database: 1,619,870
Length adjustment: 36
Effective length of query: 28
Effective length of database: 1,449,410
Effective search space: 40583480
Effective search space used: 40583480
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: 42 (22.0 bits)
S2: 123 (52.0 bits)