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= 0012.0005.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...   203   1e-53

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

 Score =  203 bits (516), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 130/238 (54%), Positives = 165/238 (69%), Gaps = 7/238 (2%)

Query: 4   LNSPDRPSAIRYLN----RVTCQGIAMSFLAGYVDTLGFVALFGLFTAHVTGNFVLIGSE 59
           L S D  +A   +N    R   Q   ++FLA YVDTLGF+ALFGLFTAHVTGNF+LIG+ 
Sbjct: 8   LESNDALTASPPMNAAAQRNRLQSSTLAFLAAYVDTLGFIALFGLFTAHVTGNFILIGAA 67

Query: 60  LANPSH-GVLIKFLAFPAFILSVVMTRLVVLALERSGKPALPWVLMLQLIFLLAFMGFGQ 118
           LA+ S   +L+KFLAFPAFIL V   RL + A++R    AL W L+LQL+ LL FM  G 
Sbjct: 68  LADSSQMSILLKFLAFPAFILGVAAARLFIAAIQRRQGRALGWSLLLQLVLLLGFMVCGV 127

Query: 119 SIAPVGVADARATAALLAGMFGAAAMGIQNAAARLILPQAAPTTVMTGNVTQLVIDVTDI 178
           + APV      A   + AG+ G A+MG+ +A +RL+L   APT++MTGNVTQ+VIDV D+
Sbjct: 128 AAAPV--QSPTAGWVMAAGLLGTASMGVHSAISRLLLAHLAPTSLMTGNVTQVVIDVVDM 185

Query: 179 VRGAADDTVRQRCVKFFWPIVAFGVGAIGGAFAYHQALFFALLLPVFILIAMIVAEFR 236
           +RGAAD    +RCVKF WP+++FGVGAI  AFAYH   F  L+ PV IL+A+IVAEFR
Sbjct: 186 LRGAADAGTTERCVKFVWPVLSFGVGAIAAAFAYHAIGFAGLIAPVLILVALIVAEFR 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
   0.331    0.141    0.417 

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: 568,207
Number of extensions: 17954
Number of successful extensions: 90
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 88
Number of HSP's successfully gapped: 1
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 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 129 (54.3 bits)