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= 0022.0298.p
         (253 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314068|ref|YP_003778160.1| permease [Herbaspirillum serope...   421   e-119

>gi|300314068|ref|YP_003778160.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 303

 Score =  421 bits (1082), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 237/253 (93%), Positives = 246/253 (97%)

Query: 1   MLDYVVLCGAAFVAGLIDAVVGGGGLVLVPTLFSVFPNTAPATLLGTNKVAGVMGTSAAA 60
           +LDY++LCGAAFVAGLIDAVVGGGGLVLVPTLFSVFP T PATLLGTNKV GVMGTSAAA
Sbjct: 51  VLDYLILCGAAFVAGLIDAVVGGGGLVLVPTLFSVFPTTTPATLLGTNKVTGVMGTSAAA 110

Query: 61  INFARKVAVRWSTVTPAAMAAFAFSFFGAYVVTHIPTDLIRKALPFVLIAVALYTLKKKD 120
           INFARKVAVRWSTVTPAAMAAFAFSFFGAYVVTHIPTDLIRKALPFVLIAVALYTLKKKD
Sbjct: 111 INFARKVAVRWSTVTPAAMAAFAFSFFGAYVVTHIPTDLIRKALPFVLIAVALYTLKKKD 170

Query: 121 FGTTHAPTLSGTREIIYAALIGGAVGFYDGVFGPGTGSFLVFLFVRVFSYDFLSASAVSK 180
           FGTTHAPTLSG+REI YAALIGGAVGFYDGVFGPGTGSFLVFLFVRVFSYDFLSASA +K
Sbjct: 171 FGTTHAPTLSGSREIFYAALIGGAVGFYDGVFGPGTGSFLVFLFVRVFSYDFLSASAAAK 230

Query: 181 FVNIATNLAALCWFGYSGHVIWQLGLLMAVFNIGGSLVGTRLAMKHGSVFVRKLFLVVVG 240
           FVN+ATNLAALCWFGYSGHVIWQLGLLMAVFN+ GSLVGT+LAMKHGSVFVRKLFLVVVG
Sbjct: 231 FVNVATNLAALCWFGYSGHVIWQLGLLMAVFNVAGSLVGTKLAMKHGSVFVRKLFLVVVG 290

Query: 241 ALILKSGYDAFLK 253
            LILKSGYDAFL+
Sbjct: 291 VLILKSGYDAFLR 303


  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    0.142    0.430 

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: 697,983
Number of extensions: 25535
Number of successful extensions: 129
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 129
Number of HSP's successfully gapped: 2
Length of query: 253
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 170
Effective length of database: 1,226,865
Effective search space: 208567050
Effective search space used: 208567050
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: 129 (54.3 bits)