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= 0034.0020.p
         (140 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310485|ref|YP_003774577.1| transcription regulator protein...    69   2e-13

>gi|300310485|ref|YP_003774577.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 145

 Score = 68.6 bits (166), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/124 (31%), Positives = 65/124 (52%), Gaps = 5/124 (4%)

Query: 10  CNLFATKQAARFITQLYERHLAPVNVTSSQVTLLAVIHERPEITMTELSEMVVMDRTSLV 69
           C     ++  R IT LY+ HL    ++ +Q +L++ I  +  I    L++ + MDR++L 
Sbjct: 6   CTCAPLRRLTRRITVLYDHHLQDCELSITQYSLISRIGRKGPIANITLAQDMGMDRSTLS 65

Query: 70  RAIQPLSRDGYV-----VQKSEAGSRKIGLSLSKAGTRKFLDALPHWRAAQKEYEELVGK 124
           RA++PL   G++        ++   R   L LS+ G  K   A P+WR AQ E + L+G 
Sbjct: 66  RALKPLMAAGWIETVDLPADAQLDKRSFALQLSQDGRAKLEQARPYWRRAQDEIDRLLGP 125

Query: 125 DRAK 128
           D A+
Sbjct: 126 DLAR 129


  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    0.129    0.356 

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: 358,000
Number of extensions: 11575
Number of successful extensions: 45
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 44
Number of HSP's successfully gapped: 1
Length of query: 140
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 64
Effective length of database: 1,260,010
Effective search space: 80640640
Effective search space used: 80640640
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: 126 (53.1 bits)