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= 0118.0002.p
         (96 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311517|ref|YP_003775609.1| tmRNA-binding protein [Herbaspi...   182   4e-48

>gi|300311517|ref|YP_003775609.1| tmRNA-binding protein
           [Herbaspirillum seropedicae SmR1]
          Length = 149

 Score =  182 bits (463), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 87/96 (90%), Positives = 92/96 (95%)

Query: 1   LFGAHISALTSTSTHVHPETTRTRKLLLNASEIDKLIGKVERSGYTLMPLNLHFSKGRIK 60
           LFG HISALTSTSTHVHPETTRTRKLLLNA+EI KLIGKVERSGYTL+PLNLH++KGRIK
Sbjct: 54  LFGCHISALTSTSTHVHPETTRTRKLLLNAAEISKLIGKVERSGYTLVPLNLHYNKGRIK 113

Query: 61  CEIGLAKGKKQHDKRETEKQRDSQREIQAAMKTHRR 96
           C+IGLAKGKKQHDKRETEKQRDSQREIQ AMK HRR
Sbjct: 114 CDIGLAKGKKQHDKRETEKQRDSQREIQTAMKQHRR 149


  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
   0.316    0.129    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: 253,335
Number of extensions: 7825
Number of successful extensions: 19
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 19
Number of HSP's successfully gapped: 1
Length of query: 96
Length of database: 1,619,870
Length adjustment: 65
Effective length of query: 31
Effective length of database: 1,312,095
Effective search space: 40674945
Effective search space used: 40674945
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 (21.6 bits)
S2: 123 (52.0 bits)