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= 0004.0178.p
         (383 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312452|ref|YP_003776544.1| permease [Herbaspirillum serope...   585   e-168

>gi|300312452|ref|YP_003776544.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 354

 Score =  585 bits (1507), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 316/352 (89%), Positives = 336/352 (95%), Gaps = 1/352 (0%)

Query: 33  TFSS-SASRGSSAWLKPLLFIVVAAIGLYYVKWSPYYLKSFVAADKHSIGASILANAPAA 91
           +FSS + +  +SAWLK LLF +VAA+GLYYVKWSPYY KSFVAADKHSIGASILANAPAA
Sbjct: 3   SFSSPTPTNKTSAWLKTLLFALVAAVGLYYVKWSPYYAKSFVAADKHSIGASILANAPAA 62

Query: 92  PWSAALEYATVYFLAIWKAAVLGVLLGSLVQVLVPRDWLLRVFGRAGLGSTLRGGLFALP 151
           PWSAALEYA +YFLAIWKAAVLG++LGSLVQVL+PRDWLLR+FGRAGLGSTLRGGLFALP
Sbjct: 63  PWSAALEYAEIYFLAIWKAAVLGIVLGSLVQVLIPRDWLLRMFGRAGLGSTLRGGLFALP 122

Query: 152 GMMCSCCAAPVVAGMRRQQVSVGAALAFWIANPVLNPATLVFMGFVLGWHFAALRLVAGV 211
           GMMCSCCAAPVVAGMRRQQVSVGAALAFWIANPVLNPATLVFMGFVLGWHFAALRLVAG+
Sbjct: 123 GMMCSCCAAPVVAGMRRQQVSVGAALAFWIANPVLNPATLVFMGFVLGWHFAALRLVAGI 182

Query: 212 LLVVGVSLIAQRVAQTETLPQAALDAVAAAEYEPMDDGRHFLVRWGSKLWQLFWTTAPVY 271
           LLV+GV+LIAQRVAQ+ETLPQAA+DA+AAAEYEP++DGRHFLVRWGSKLWQLFWTTAPVY
Sbjct: 183 LLVLGVALIAQRVAQSETLPQAAMDALAAAEYEPLEDGRHFLVRWGSKLWQLFWTTAPVY 242

Query: 272 IVVVLALGAARVWLFPQVDASMGNSLLWIVALAVVGTLFVIPTAAEIPIVQSMLSLGMGV 331
           IV VLALGAARVWLFPQVD +MGNSLLWIVALAVVGTLFVIPTAAEIPIVQSMLSLGMGV
Sbjct: 243 IVAVLALGAARVWLFPQVDVAMGNSLLWIVALAVVGTLFVIPTAAEIPIVQSMLSLGMGV 302

Query: 332 GPAVALLMTLPSISLPSLLMLRKSFTPRVLTTVTLLTMLIGVVSGLVAVVLL 383
           GPAVALLMTLPSISLPSLLMLR SFT RVLTTVTLLTMLIG  SGL AV LL
Sbjct: 303 GPAVALLMTLPSISLPSLLMLRHSFTSRVLTTVTLLTMLIGAASGLAAVALL 354


  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    0.138    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: 964,142
Number of extensions: 35294
Number of successful extensions: 190
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 190
Number of HSP's successfully gapped: 1
Length of query: 383
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 296
Effective length of database: 1,207,925
Effective search space: 357545800
Effective search space used: 357545800
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: 131 (55.1 bits)