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= 0001.3118.p
         (355 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...   574   e-165

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

 Score =  574 bits (1479), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/353 (87%), Positives = 329/353 (93%)

Query: 3   SSSSLPSSPRGASAWLKPLLFILVAAIGLYYVKWSPYYLKSFVAADKHSIGNSILANAPA 62
           SS S P+     SAWLK LLF LVAA+GLYYVKWSPYY KSFVAADKHSIG SILANAPA
Sbjct: 2   SSFSSPTPTNKTSAWLKTLLFALVAAVGLYYVKWSPYYAKSFVAADKHSIGASILANAPA 61

Query: 63  APWSAALEYAGVYFLAIWKAAVLGVLLGSLVQVLVPRDWLLRVFGRAGLGSTIRGGLFAL 122
           APWSAALEYA +YFLAIWKAAVLG++LGSLVQVL+PRDWLLR+FGRAGLGST+RGGLFAL
Sbjct: 62  APWSAALEYAEIYFLAIWKAAVLGIVLGSLVQVLIPRDWLLRMFGRAGLGSTLRGGLFAL 121

Query: 123 PGMMCSCCAAPVVAGMRRQQVSVGAALAFWIANPVLNPATLVFMGFVLGWNFAALRLVAG 182
           PGMMCSCCAAPVVAGMRRQQVSVGAALAFWIANPVLNPATLVFMGFVLGW+FAALRLVAG
Sbjct: 122 PGMMCSCCAAPVVAGMRRQQVSVGAALAFWIANPVLNPATLVFMGFVLGWHFAALRLVAG 181

Query: 183 VLLVLGVALIAQRVAQAETLPQAALDAVAAAEYEPLDDGRPFLLRWAGKLWQLFWTTIPV 242
           +LLVLGVALIAQRVAQ+ETLPQAA+DA+AAAEYEPL+DGR FL+RW  KLWQLFWTT PV
Sbjct: 182 ILLVLGVALIAQRVAQSETLPQAAMDALAAAEYEPLEDGRHFLVRWGSKLWQLFWTTAPV 241

Query: 243 YIVVVLALGAARVWLFPQVDASMGNSLLWIVTLAVIGTLFVIPTAAEIPIVQSMLSLGMG 302
           YIV VLALGAARVWLFPQVD +MGNSLLWIV LAV+GTLFVIPTAAEIPIVQSMLSLGMG
Sbjct: 242 YIVAVLALGAARVWLFPQVDVAMGNSLLWIVALAVVGTLFVIPTAAEIPIVQSMLSLGMG 301

Query: 303 VGPAVALLMTLPSISLPSLLMLRTSFTRRVLVTVTLLTILIGAASGLVAVVVL 355
           VGPAVALLMTLPSISLPSLLMLR SFT RVL TVTLLT+LIGAASGL AV +L
Sbjct: 302 VGPAVALLMTLPSISLPSLLMLRHSFTSRVLTTVTLLTMLIGAASGLAAVALL 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    0.139    0.429 

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: 863,036
Number of extensions: 31636
Number of successful extensions: 185
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 185
Number of HSP's successfully gapped: 1
Length of query: 355
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 269
Effective length of database: 1,212,660
Effective search space: 326205540
Effective search space used: 326205540
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)