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= 042298
         (186 letters)

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

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



>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
          Length = 268

 Score = 29.6 bits (65), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 23  ATTLNKNNNVKREDDTRV--TSLSFGISEA--AGGLRNGKCNFSPRPRPLLCRISQLEVA 78
            T L ++N V    D  +  T L  GI E      LR GKC+F P  R  + R+    + 
Sbjct: 137 ETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLV 196

Query: 79  D 79
           D
Sbjct: 197 D 197


>pdb|2LOO|A Chain A, Backbone Structure Of Human Membrane Protein Tmem14a From
           Noe Data
 pdb|2LOP|A Chain A, Backbone Structure Of Human Membrane Protein Tmem14a
          Length = 108

 Score = 26.6 bits (57), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 20/29 (68%)

Query: 142 SAFLFSSVFGIRLVATQRPIPAGPLLGLS 170
           +AF  +++ G+R   +++ +PAG + GLS
Sbjct: 68  TAFFLATIMGVRFKRSKKIMPAGLVAGLS 96


  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
   0.320    0.133    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,326,662
Number of Sequences: 62578
Number of extensions: 134585
Number of successful extensions: 249
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: 248
Number of HSP's gapped (non-prelim): 2
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)