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= 0002.0044.p
         (257 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312398|ref|YP_003776490.1| permease [Herbaspirillum serope...   487   e-139

>gi|300312398|ref|YP_003776490.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 257

 Score =  487 bits (1254), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 256/257 (99%), Positives = 257/257 (100%)

Query: 1   MTVSYVVSGFAVGLLVGLTGVGGGSLMTPLLTLLFGIHPSVAVGTDLAFASATKTAGTLA 60
           MTVSYVVSGFAVGLLVGLTGVGGGSLMTPLLTLLFGIHPSVAVGTDLAFASATKTAGTLA
Sbjct: 1   MTVSYVVSGFAVGLLVGLTGVGGGSLMTPLLTLLFGIHPSVAVGTDLAFASATKTAGTLA 60

Query: 61  HRFKGTVRWDVVRRLSYGALPAALITTLLLKHFGAVSDGIALTIRYSIAISVFLTVIALL 120
           HRFKGTVRWDVVRRLSYGALPAALITTLLLKHFGAVSDGIALTIRYSIA+SVFLTVIALL
Sbjct: 61  HRFKGTVRWDVVRRLSYGALPAALITTLLLKHFGAVSDGIALTIRYSIAVSVFLTVIALL 120

Query: 121 FRSRMQAWLNAHPQRQLQGATLANATIAAGALLGTLVTISSIGAGAVGATLLVLLYPRLS 180
           FRSRMQAWLNAHPQRQLQGATLANATIAAGALLGTLVTISSIGAGAVGATLLVLLYPRLS
Sbjct: 121 FRSRMQAWLNAHPQRQLQGATLANATIAAGALLGTLVTISSIGAGAVGATLLVLLYPRLS 180

Query: 181 PAEIAGTDIAYAVPLTAIAALGHWWLGSINWELLATLLLGSVPGITIGSLAARAVPEKFL 240
           PAEIAGTDIAYAVPLTAIAALGHWWLGSINWELLATLLLGSVPGITIGSLAARAVPEKFL
Sbjct: 181 PAEIAGTDIAYAVPLTAIAALGHWWLGSINWELLATLLLGSVPGITIGSLAARAVPEKFL 240

Query: 241 RGLLAITLTSVAVKLIW 257
           RGLLAITLTSVAVKLIW
Sbjct: 241 RGLLAITLTSVAVKLIW 257


  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
   0.324    0.138    0.406 

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: 606,879
Number of extensions: 20806
Number of successful extensions: 161
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 2
Length of query: 257
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 174
Effective length of database: 1,226,865
Effective search space: 213474510
Effective search space used: 213474510
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 129 (54.3 bits)