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= 0028.0099.p
         (139 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311231|ref|YP_003775323.1| recombination factor RarA prote...   219   9e-59
gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alph...    62   2e-11

>gi|300311231|ref|YP_003775323.1| recombination factor RarA protein
           [Herbaspirillum seropedicae SmR1]
          Length = 434

 Score =  219 bits (557), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 102/107 (95%), Positives = 105/107 (98%)

Query: 33  LYLAVAAKSNAGYNAYNAARAFVKQDKSREVPVHLRNAPTKLMKELGYGHEYRYAHDEPN 92
           +YLAVAAKSNAGYNAYNAARAFVKQDKSREVPVHLRNAPTKLMKELGYGHEYRYAHDEPN
Sbjct: 328 IYLAVAAKSNAGYNAYNAARAFVKQDKSREVPVHLRNAPTKLMKELGYGHEYRYAHDEPN 387

Query: 93  AYAAGETYLPDGIAEPGWYQPVPRGLEIKIGEKLMTLRQWDEDARKN 139
           AYAAGETYLPDGI EPGWYQPVPRGLEIKIGEKL TLRQWDE+ARK+
Sbjct: 388 AYAAGETYLPDGIEEPGWYQPVPRGLEIKIGEKLATLRQWDEEARKD 434


>gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alpha
           [Herbaspirillum seropedicae SmR1]
          Length = 942

 Score = 61.6 bits (148), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/39 (74%), Positives = 34/39 (87%)

Query: 1   VQECGLSLAPNAEQHLRPRMRLSLVHSPATLALYLAVAA 39
           VQECG +LAPNAEQHLR R+RL +VH+PATLA  LA+AA
Sbjct: 238 VQECGHALAPNAEQHLRSRVRLGMVHTPATLAQTLAIAA 276


  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    0.132    0.399 

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: 420,694
Number of extensions: 15815
Number of successful extensions: 32
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 32
Number of HSP's successfully gapped: 2
Length of query: 139
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 63
Effective length of database: 1,260,010
Effective search space: 79380630
Effective search space used: 79380630
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: 126 (53.1 bits)