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= 0241.0008.p
         (128 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313603|ref|YP_003777695.1| membrane protein [Herbaspirillu...   122   1e-29

>gi|300313603|ref|YP_003777695.1| membrane protein [Herbaspirillum
           seropedicae SmR1]
          Length = 349

 Score =  122 bits (305), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 74/120 (61%), Positives = 91/120 (75%), Gaps = 5/120 (4%)

Query: 1   VITKMVRVMMLAPFLLVLSAYVRRDRAVAATGKSANTSRLAGVPWFAFAFIGMVALNSLL 60
           VITKMVRVMMLAPFLL+LS       A   +G     ++L+ +PWFAFAFIG+V  NS  
Sbjct: 227 VITKMVRVMMLAPFLLMLS----MKAAPTTSGHQHQHNKLS-IPWFAFAFIGVVVFNSFF 281

Query: 61  PIPAAATGALLDADTFLLAMAMAALGLTTHLSSVRRAGMRPLLLGGMLFAWLVVGGAAVN 120
           P+PAA    LL ADT +LAMAMAALGL+THLS++R AG++P++LG +LFAWLVVGGA VN
Sbjct: 282 PLPAALNQLLLQADTLMLAMAMAALGLSTHLSALRSAGIKPMILGAVLFAWLVVGGALVN 341


  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
   0.331    0.137    0.403 

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: 248,939
Number of extensions: 6088
Number of successful extensions: 54
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 53
Number of HSP's successfully gapped: 1
Length of query: 128
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 53
Effective length of database: 1,264,745
Effective search space: 67031485
Effective search space used: 67031485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 125 (52.8 bits)