BLASTP 2.2.26 [Sep-21-2011]


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= 018727
         (351 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|2GFP|A Chain A, Structure Of The Multidrug Transporter Emrd From
           Escherichia Coli
 pdb|2GFP|B Chain B, Structure Of The Multidrug Transporter Emrd From
           Escherichia Coli
          Length = 375

 Score = 35.4 bits (80), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 7/73 (9%)

Query: 62  PFLYFMIKDFQIAKREEDIGSYAGYVGSSFMFGRALTSVFWGLVADRYGRKPVIIMGTAS 121
           P +  M +D  +  RE  + S  G    +++    ++ +F+G ++DR GR+PVI++G  S
Sbjct: 21  PAIADMARDLNV--REGAVQSVMG----AYLLTYGVSQLFYGPISDRVGRRPVILVGM-S 73

Query: 122 VVIFNTLFGLSVN 134
           + +  TL  ++ +
Sbjct: 74  IFMLATLVAVTTS 86


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.324    0.140    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,339,833
Number of Sequences: 62578
Number of extensions: 337566
Number of successful extensions: 715
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 714
Number of HSP's gapped (non-prelim): 2
length of query: 351
length of database: 14,973,337
effective HSP length: 100
effective length of query: 251
effective length of database: 8,715,537
effective search space: 2187599787
effective search space used: 2187599787
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)