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= 0001.2405.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|300310130|ref|YP_003774222.1| type III secretion HrcS protein...   156   2e-40

>gi|300310130|ref|YP_003774222.1| type III secretion HrcS protein
          [Herbaspirillum seropedicae SmR1]
          Length = 87

 Score =  156 bits (395), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 76/87 (87%), Positives = 84/87 (96%)

Query: 1  MADTLNFFQQGLWMAVMMSAPPLVIATLCGVVVSLIQAVTQIQDQTLPYVVKLMAVAVTL 60
          MADT+NFFQQ LWMA+MMSAPPL+IATLCG+ VSLIQAVTQIQDQTLPYVVKL+AVAVTL
Sbjct: 1  MADTINFFQQSLWMAIMMSAPPLLIATLCGLGVSLIQAVTQIQDQTLPYVVKLVAVAVTL 60

Query: 61 ATMGRWIGVELLRLADMAMTMVPDIGR 87
          A+MGRWIGVE+LRLAD+A TMVPDIGR
Sbjct: 61 ASMGRWIGVEMLRLADLAFTMVPDIGR 87


  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
   0.329    0.137    0.406 

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: 225,980
Number of extensions: 5919
Number of successful extensions: 44
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 44
Number of HSP's successfully gapped: 2
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 123 (52.0 bits)