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= 0002.0051.p
         (121 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309482|ref|YP_003773574.1| DNA-directed RNA polymerase sub...   175   9e-46

>gi|300309482|ref|YP_003773574.1| DNA-directed RNA polymerase
           subunit alpha [Herbaspirillum seropedicae SmR1]
          Length = 325

 Score =  175 bits (443), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 88/94 (93%), Positives = 88/94 (93%), Gaps = 1/94 (1%)

Query: 1   VFAALEGTEATAEAPSRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENE 60
           VFAALEGTEATAEAPSRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENE
Sbjct: 226 VFAALEGTEATAEAPSRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENE 285

Query: 61  LLKTPNLGRKSLNEIKEVLASRGLTXLAMMAGGW 94
           LLKTPNLGRKSLNEIKEVLASRGLT L M    W
Sbjct: 286 LLKTPNLGRKSLNEIKEVLASRGLT-LGMKLENW 318


  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
   0.312    0.129    0.363 

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: 243,270
Number of extensions: 6741
Number of successful extensions: 32
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 32
Number of HSP's successfully gapped: 1
Length of query: 121
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 47
Effective length of database: 1,269,480
Effective search space: 59665560
Effective search space used: 59665560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 125 (52.8 bits)