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= 0058.0001.p
         (204 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314041|ref|YP_003778133.1| transporter permease [Herbaspir...    55   4e-09

>gi|300314041|ref|YP_003778133.1| transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 311

 Score = 55.1 bits (131), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 54/192 (28%), Positives = 90/192 (46%), Gaps = 9/192 (4%)

Query: 2   YNNGGNMGVPLMLLAFGPESLSAAVALFTAATFVYFSLGIKMLQ---HGRDTRPGSFLK- 57
           Y N G +G+PL  LAFG + L  +V        + F++ I +L+   H +     +  K 
Sbjct: 103 YANVGFIGIPLCYLAFGHDGLPPSVIAMVMTACLLFAVAIVLLETCLHAQAGLAHTVAKV 162

Query: 58  ---LFKSPIMVAMVLGVLFAVLHVPLPQPLFSAMKLLGEASIPIMLFALGVRMMD--ISF 112
              L ++PIM+A V G++ AV  +P+P  +    K+LG A+ P  L +LG+ +       
Sbjct: 163 GRSLLRNPIMIAPVAGIIVAVFGLPVPSGVQQLFKILGGAAGPCALVSLGLFLAQPVQDR 222

Query: 113 KSWHIGLVGAVTCPLVGLIVAFALDQVLPLTSGQRGQMYLFGALPPAVLCFMVAEQYRQE 172
           +   + L+ A    L   I A     +LPL         L  A+P     FM+AE Y++E
Sbjct: 223 QGASVSLLVAFKLLLQPAITAVLAYWLLPLPRLWADAAVLLSAMPIGTGPFMLAELYQRE 282

Query: 173 PDKVAAIVLMGN 184
              ++  +L+  
Sbjct: 283 VTAMSRAILVST 294


  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    0.144    0.436 

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: 643,325
Number of extensions: 26369
Number of successful extensions: 137
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 136
Number of HSP's successfully gapped: 1
Length of query: 204
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 123
Effective length of database: 1,236,335
Effective search space: 152069205
Effective search space used: 152069205
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 (21.8 bits)
S2: 128 (53.9 bits)