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= 0001.4398.p
         (249 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...   364   e-102

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

 Score =  364 bits (935), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 210/247 (85%), Positives = 224/247 (90%), Gaps = 4/247 (1%)

Query: 7   PPSSTQ----ARPTLMNVAQRNCLQSSGLAFLAAYVDTLGFIALFGLFTAHVTGNFILIG 62
           PP  +     A P +   AQRN LQSS LAFLAAYVDTLGFIALFGLFTAHVTGNFILIG
Sbjct: 6   PPLESNDALTASPPMNAAAQRNRLQSSTLAFLAAYVDTLGFIALFGLFTAHVTGNFILIG 65

Query: 63  AALADTSQMSILLKFLAFPAFILGVAVARVFIAAIQRAHGRALAWSLLLQLVLLIGFMLC 122
           AALAD+SQMSILLKFLAFPAFILGVA AR+FIAAIQR  GRAL WSLLLQLVLL+GFM+C
Sbjct: 66  AALADSSQMSILLKFLAFPAFILGVAAARLFIAAIQRRQGRALGWSLLLQLVLLLGFMVC 125

Query: 123 GIAAAPVQSPTAGWVMAAGLLGTASMGVHNAISRLLLSHLAPTSLMTGNVTQVVIDMVDM 182
           G+AAAPVQSPTAGWVMAAGLLGTASMGVH+AISRLLL+HLAPTSLMTGNVTQVVID+VDM
Sbjct: 126 GVAAAPVQSPTAGWVMAAGLLGTASMGVHSAISRLLLAHLAPTSLMTGNVTQVVIDVVDM 185

Query: 183 LRGAADAGTTERCVKFVWPVLSFGVGAIAAAFAYHAIGFAGLIVPVLILVAMIVWEWRQP 242
           LRGAADAGTTERCVKFVWPVLSFGVGAIAAAFAYHAIGFAGLI PVLILVA+IV E+RQP
Sbjct: 186 LRGAADAGTTERCVKFVWPVLSFGVGAIAAAFAYHAIGFAGLIAPVLILVALIVAEFRQP 245

Query: 243 APSALAK 249
            P+  A+
Sbjct: 246 LPADSAR 252


  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    0.138    0.421 

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: 652,413
Number of extensions: 21573
Number of successful extensions: 135
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 135
Number of HSP's successfully gapped: 1
Length of query: 249
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 166
Effective length of database: 1,226,865
Effective search space: 203659590
Effective search space used: 203659590
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)