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= 0002.0175.p
         (228 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310791|ref|YP_003774883.1| solute binding periplasmic prot...    92   3e-20

>gi|300310791|ref|YP_003774883.1| solute binding periplasmic protein
           [Herbaspirillum seropedicae SmR1]
          Length = 262

 Score = 92.0 bits (227), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 116/234 (49%), Gaps = 16/234 (6%)

Query: 1   VLAAGAIAPIVRTVAADFERRSGIHVTVDN------ATGGVVDKRVRSGAAADVVVAPDG 54
           V+++G  A   +T+A +FE+++G H  +         T   +  R++ G   DVV+    
Sbjct: 33  VVSSGGFAAAYKTLAPEFEKKTG-HKLISGWGPSMGETPQAIPNRLQRGEHIDVVIMVGD 91

Query: 55  VLRGLGKDGYLNLASERPIARVGIAVAVRQGAPSPAIATVAQFRKALLDAPSVAVIDPKA 114
            L  L   G ++    + +A   I +AV+ GAP P I+ +  F++ LL A SV   D   
Sbjct: 92  SLDKLVAAGKVSKTEHKLLALSRIGLAVKAGAPRPDISNLDAFKRTLLTAHSVVYSD--- 148

Query: 115 GGSSGIYLE-KLFERLGIASQMHAKEVLVPGGLVAEKLVDGSAALALHQQSEILLVKGAK 173
             +SG++L  KLF+RLGI  QM  K  ++P   V + +  G A + L Q SE+  VKG  
Sbjct: 149 -SASGVFLSTKLFKRLGIDQQMAYKGRMIPAEPVGQVVARGDAEIGLQQISELKPVKGID 207

Query: 174 LVGPLPADIQNYTVYVG--AVGARTASGATGRAFLTMFGEETARRAMVEHGLLP 225
           ++GP+P + Q  T +     VGA  A  A  +  +       A+ A+   GL P
Sbjct: 208 IIGPIPEEAQQLTPFSAGVVVGAHEAEAA--KELVHFLASPEAQAAIKASGLDP 259


  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
   0.318    0.135    0.375 

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: 646,272
Number of extensions: 25223
Number of successful extensions: 105
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 1
Length of query: 228
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 146
Effective length of database: 1,231,600
Effective search space: 179813600
Effective search space used: 179813600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 129 (54.3 bits)