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= 0001.4307.p
         (87 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313854|ref|YP_003777946.1| LysR family transcription regul...    62   1e-11

>gi|300313854|ref|YP_003777946.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 310

 Score = 62.0 bits (149), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 39/97 (40%), Positives = 50/97 (51%), Gaps = 14/97 (14%)

Query: 1   LHSERYARTLHRRQTTR-----TSMVVAGHGLGWMPESCVEREIAEKRLVVA---GDSQ- 51
           LHS      L RR  T       SM V GHG+ W+P S V REIAE +L +A    DS+ 
Sbjct: 214 LHSSPRQVHLFRRFETDLAEGLKSMAVEGHGIAWLPASAVAREIAEGKLTLAIAPTDSEA 273

Query: 52  -----WRSPLEIRLYRAADCSNEFIDRLWAFLLTSHA 83
                W   ++IR+YR  D +N  IDR+W +L   H 
Sbjct: 274 LEQGLWCDEMDIRVYRRLDGANPDIDRIWNYLKAEHG 310


  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
   0.322    0.131    0.414 

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: 280,395
Number of extensions: 9215
Number of successful extensions: 29
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 29
Number of HSP's successfully gapped: 1
Length of query: 87
Length of database: 1,619,870
Length adjustment: 57
Effective length of query: 30
Effective length of database: 1,349,975
Effective search space: 40499250
Effective search space used: 40499250
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 (22.0 bits)
S2: 123 (52.0 bits)