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= 0027.0114.p
         (160 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313514|ref|YP_003777606.1| transcription regulator protein...   162   1e-41

>gi|300313514|ref|YP_003777606.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 159

 Score =  162 bits (410), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 84/139 (60%), Positives = 101/139 (72%), Gaps = 1/139 (0%)

Query: 1   VTNRKFDRKEVRISTFDPANYLDSKETITAYLQTALEENDPDFLMAALNDVIRAQGIAEV 60
           +T RKF  K++++S FDP  YLDS E I AYL+ AL ENDP FLMAALNDVIRA+G+A++
Sbjct: 1   MTARKFSTKDLQVSAFDPVTYLDSDEAIAAYLEIALAENDPVFLMAALNDVIRARGVADI 60

Query: 61  AGKAGLGRESLYKTLKPGAEPRLGTVLRLLGALDLRLSIAAPQGGRKAKRSGTVKTSSAQ 120
           A KAGLGRESLYKTLKPGA PRL TVL+LLGALD+RLSI   +  R AK++ + K S+A 
Sbjct: 61  ASKAGLGRESLYKTLKPGAHPRLSTVLQLLGALDIRLSITPAKSARTAKKTAS-KKSAAT 119

Query: 121 APATKKPAPRRAAITKMIP 139
             A     P R    KM P
Sbjct: 120 KRARMTSTPGRPVQAKMAP 138


  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
   0.313    0.130    0.359 

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: 391,754
Number of extensions: 11762
Number of successful extensions: 39
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 38
Number of HSP's successfully gapped: 1
Length of query: 160
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 82
Effective length of database: 1,250,540
Effective search space: 102544280
Effective search space used: 102544280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 127 (53.5 bits)