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= 0216.0025.p
         (243 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313790|ref|YP_003777882.1| permease [Herbaspirillum serope...   209   1e-55

>gi|300313790|ref|YP_003777882.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 253

 Score =  209 bits (533), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 133/236 (56%), Positives = 167/236 (70%), Gaps = 5/236 (2%)

Query: 2   DALNSAGRPTAFRYLNRATCQGIAMSFLAGYVDTLGFVALFGLFTAHVTGNFVLIGSELA 61
           DAL ++    A    NR   Q   ++FLA YVDTLGF+ALFGLFTAHVTGNF+LIG+ LA
Sbjct: 12  DALTASPPMNAAAQRNR--LQSSTLAFLAAYVDTLGFIALFGLFTAHVTGNFILIGAALA 69

Query: 62  NPSH-GVLIKFLAFPAFILSVVMTRLVVIALERSGKPALPWVLMLQLVFLLAFMGLGQSM 120
           + S   +L+KFLAFPAFIL V   RL + A++R    AL W L+LQLV LL FM  G + 
Sbjct: 70  DSSQMSILLKFLAFPAFILGVAAARLFIAAIQRRQGRALGWSLLLQLVLLLGFMVCGVAA 129

Query: 121 APVNVTDARAIGVLLAGMLGAAAMGIQNAAARLILPQAAPTTVMTGNVTQLVIDVTDIVR 180
           APV    A    V+ AG+LG A+MG+ +A +RL+L   APT++MTGNVTQ+VIDV D++R
Sbjct: 130 APVQSPTAG--WVMAAGLLGTASMGVHSAISRLLLAHLAPTSLMTGNVTQVVIDVVDMLR 187

Query: 181 GAADDAVRQRCIKFFWPIVAFGVGAIGGAFAYRQALFLALLLPVLILVAMIVAEFR 236
           GAAD    +RC+KF WP+++FGVGAI  AFAY    F  L+ PVLILVA+IVAEFR
Sbjct: 188 GAADAGTTERCVKFVWPVLSFGVGAIAAAFAYHAIGFAGLIAPVLILVALIVAEFR 243


  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
   0.330    0.141    0.412 

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: 551,799
Number of extensions: 19348
Number of successful extensions: 97
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 96
Number of HSP's successfully gapped: 2
Length of query: 243
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 160
Effective length of database: 1,226,865
Effective search space: 196298400
Effective search space used: 196298400
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 (21.9 bits)
S2: 129 (54.3 bits)