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= 0001.3856.p
         (120 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313261|ref|YP_003777353.1| sigma-54 modulation protein [He...   174   1e-45

>gi|300313261|ref|YP_003777353.1| sigma-54 modulation protein
          [Herbaspirillum seropedicae SmR1]
          Length = 108

 Score =  174 bits (442), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 87/88 (98%), Positives = 88/88 (100%)

Query: 1  MNLTISGHHLELTPAIREYVQSKLSRIKRHFDNVIDVSVILSVDKLTEKEKRQKAEINVH 60
          MNLTISGHHLELTPAIREYVQSKL+RIKRHFDNVIDVSVILSVDKLTEKEKRQKAEINVH
Sbjct: 1  MNLTISGHHLELTPAIREYVQSKLARIKRHFDNVIDVSVILSVDKLTEKEKRQKAEINVH 60

Query: 61 IKGKDLHAESIAHDLYAAIDALIDKLDR 88
          IKGKDLHAESIAHDLYAAIDALIDKLDR
Sbjct: 61 IKGKDLHAESIAHDLYAAIDALIDKLDR 88


  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
   0.317    0.132    0.361 

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: 339,274
Number of extensions: 11291
Number of successful extensions: 40
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 40
Number of HSP's successfully gapped: 1
Length of query: 120
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 46
Effective length of database: 1,269,480
Effective search space: 58396080
Effective search space used: 58396080
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 (21.7 bits)
S2: 125 (52.8 bits)