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= 016412
         (390 letters)

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

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



>pdb|2K0L|A Chain A, Nmr Structure Of The Transmembrane Domain Of The Outer
           Membrane Protein A From Klebsiella Pneumoniae In Dhpc
           Micelles
          Length = 216

 Score = 30.4 bits (67), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 303 AKRNIKKSEDDIPVPPLVKSAALWGVFLAVSSNIRYQIVNGLERIVESSPLAKQLPPVAM 362
           A   + +SE D  V P+      W V   +++ + YQ VN    I ++  +  +     +
Sbjct: 128 ASTGVSRSEHDTGVSPVFAGGVEWAVTRDIATRLEYQWVN---NIGDAGTVGTRPDNGML 184

Query: 363 AFTVGVRFA 371
           +  V  RF 
Sbjct: 185 SLGVSYRFG 193


  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
   0.323    0.139    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,324,847
Number of Sequences: 62578
Number of extensions: 381497
Number of successful extensions: 685
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 684
Number of HSP's gapped (non-prelim): 1
length of query: 390
length of database: 14,973,337
effective HSP length: 101
effective length of query: 289
effective length of database: 8,652,959
effective search space: 2500705151
effective search space used: 2500705151
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)