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= 0002.0555.p
         (112 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310408|ref|YP_003774500.1| LysR family transcription regul...    59   9e-11

>gi|300310408|ref|YP_003774500.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 296

 Score = 58.9 bits (141), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 44/78 (56%), Gaps = 3/78 (3%)

Query: 1   VSSNGVSTSPDWRFTKGGATTIVRVQPRMTVMSNDEAIIAALDGFGITRVLSYMVAAPLS 60
           V+S     SP+WRF  G     V V+  +   +N+ AI  A  G+G+TRVL+Y VAA L 
Sbjct: 190 VTSTSAWASPEWRFADGQR---VLVEAALQTNTNEAAIATARQGWGLTRVLAYQVAADLQ 246

Query: 61  DGRLVEVLHGHETPTLPV 78
            GRL  V+   E P LP+
Sbjct: 247 AGRLQRVMSEFEEPPLPI 264


  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
   0.318    0.128    0.375 

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: 359,778
Number of extensions: 13039
Number of successful extensions: 57
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 56
Number of HSP's successfully gapped: 1
Length of query: 112
Length of database: 1,619,870
Length adjustment: 73
Effective length of query: 39
Effective length of database: 1,274,215
Effective search space: 49694385
Effective search space used: 49694385
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: 41 (21.8 bits)
S2: 124 (52.4 bits)