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= 0002.0303.p
         (275 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alph...   115   3e-27

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

 Score =  115 bits (289), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 61/87 (70%), Positives = 69/87 (79%), Gaps = 2/87 (2%)

Query: 1   MGFYSPSQLIQDARRHSVRVLPADVMHSNWESTLE--DLRAARPAVRLGLSLLGGMKEEA 58
           MGFYSPSQLIQDARRH V+VLPA+V+ S WESTLE      ARPAVRLGLSLL  M  EA
Sbjct: 793 MGFYSPSQLIQDARRHGVQVLPANVVRSRWESTLELPSSAGARPAVRLGLSLLRSMPAEA 852

Query: 59  ALRIEQARRTQVFSDIQELARRAGLDK 85
           A RIEQAR  + F+D+ +LARRAGLD+
Sbjct: 853 AQRIEQARAQRPFADVDDLARRAGLDR 879


  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
   0.321    0.135    0.391 

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: 880,692
Number of extensions: 36752
Number of successful extensions: 119
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 118
Number of HSP's successfully gapped: 1
Length of query: 275
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 191
Effective length of database: 1,222,130
Effective search space: 233426830
Effective search space used: 233426830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 130 (54.7 bits)