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= 0002.0257.p
         (308 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314041|ref|YP_003778133.1| transporter permease [Herbaspir...    64   1e-11

>gi|300314041|ref|YP_003778133.1| transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 311

 Score = 63.9 bits (154), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 83/301 (27%), Positives = 138/301 (45%), Gaps = 29/301 (9%)

Query: 7   ITGIILPVFAIIAIGYGYARWRGEVVRSDMASVNRVSMEVLAPLMVF---SALSAKDF-D 62
           I  I+ PVF++I +G+   R R  +       +NR  + +  P ++F   S LSA DF +
Sbjct: 4   IFNIVFPVFSLIFLGWA-CRKRNILSGGAATELNRFVIWLALPALLFDSMSRLSAADFAN 62

Query: 63  LAHNGWLILASVIISLGSALLAW---PVATMLGYDKRTFLPPMMYNNGGNMGVPLMLLAF 119
           L       L++ ++ L +A L W     A  +  D         Y N G +G+PL  LAF
Sbjct: 63  LRFIAVFALSTALVFLLTAWLRWRERAAAADIIIDSLG----SAYANVGFIGIPLCYLAF 118

Query: 120 GPESLSAAVALFTAATFVYFSLGIRMLQ---HGRA----ITTRPGSFLKLFKSPIMVAMV 172
           G + L  +V        + F++ I +L+   H +A       + G    L ++PIM+A V
Sbjct: 119 GHDGLPPSVIAMVMTACLLFAVAIVLLETCLHAQAGLAHTVAKVGR--SLLRNPIMIAPV 176

Query: 173 LGVLFAVLHVPLPPPVFSAMKLLGEASIPIMLFALGVRMMD--ISFKSWHIGLVGAVTC- 229
            G++ AV  +P+P  V    K+LG A+ P  L +LG+ +       +   + L+ A    
Sbjct: 177 AGIIVAVFGLPVPSGVQQLFKILGGAAGPCALVSLGLFLAQPVQDRQGASVSLLVAFKLL 236

Query: 230 --PLVGLAVAFALDQALPLTAGQRGQMYLFGALPPAVLCFMVAEQYRQEPDKVASIVLMG 287
             P +   +A+ L   LPL         L  A+P     FM+AE Y++E   ++  +L+ 
Sbjct: 237 LQPAITAVLAYWL---LPLPRLWADAAVLLSAMPIGTGPFMLAELYQREVTAMSRAILVS 293

Query: 288 N 288
            
Sbjct: 294 T 294


  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    0.432 

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: 958,506
Number of extensions: 38931
Number of successful extensions: 217
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 213
Number of HSP's successfully gapped: 2
Length of query: 308
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 223
Effective length of database: 1,217,395
Effective search space: 271479085
Effective search space used: 271479085
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: 130 (54.7 bits)