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= 0020.0178.p
         (259 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...   119   2e-28

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

 Score =  119 bits (299), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 87/236 (36%), Positives = 133/236 (56%), Gaps = 9/236 (3%)

Query: 26  ALMTPILLIFFGHSPATAIATDLWFAAITKLVGARMHYAQGNVDWQVAKRLWLGSLPMAL 85
           +LMTP+L + FG  P+ A+ TDL FA+ TK  G   H  +G V W V +RL  G+LP AL
Sbjct: 25  SLMTPLLTLLFGIHPSVAVGTDLAFASATKTAGTLAHRFKGTVRWDVVRRLSYGALPAAL 84

Query: 86  LMVFIVGLGGRLIKMEWLT--QAIGVVVLMTATGLLAAPTLAACARRWRIEQPER--FKA 141
           +   ++   G +     LT   +I V V +T   LL    + A    W    P+R    A
Sbjct: 85  ITTLLLKHFGAVSDGIALTIRYSIAVSVFLTVIALLFRSRMQA----WLNAHPQRQLQGA 140

Query: 142 VQPALTMAAGAVLGLSVALTSVGAGALGSVMLLYLYPLRMTPHRLVATDIVHAIPLALVA 201
                T+AAGA+LG  V ++S+GAGA+G+ +L+ LYP R++P  +  TDI +A+PL  +A
Sbjct: 141 TLANATIAAGALLGTLVTISSIGAGAVGATLLVLLYP-RLSPAEIAGTDIAYAVPLTAIA 199

Query: 202 GSAYLLAGLVDEWMLLSLLTGSVPAVLLGSLLAGKMAGRALQIALALVLLAGGLKV 257
              +   G ++  +L +LL GSVP + +GSL A  +  + L+  LA+ L +  +K+
Sbjct: 200 ALGHWWLGSINWELLATLLLGSVPGITIGSLAARAVPEKFLRGLLAITLTSVAVKL 255


  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
   0.327    0.140    0.420 

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: 662,584
Number of extensions: 25183
Number of successful extensions: 192
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 1
Length of query: 259
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 176
Effective length of database: 1,226,865
Effective search space: 215928240
Effective search space used: 215928240
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 (21.7 bits)
S2: 129 (54.3 bits)