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= 027293
         (225 letters)

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

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



>pdb|4DXW|A Chain A, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
 pdb|4DXW|B Chain B, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
 pdb|4DXW|C Chain C, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
 pdb|4DXW|D Chain D, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
          Length = 229

 Score = 27.7 bits (60), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 25/47 (53%)

Query: 97  RLIRVIQAFQTRIGARIQELRKDFPTKLLFFLVGFYCATAFATVIGQ 143
           RLI VI   +  I A ++ +R+ F   LL F++ +  AT  A + G 
Sbjct: 111 RLISVIPELKQIIEAILESVRRVFFVSLLLFIILYIYATMGAILFGN 157


  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
   0.328    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: 6,259,651
Number of Sequences: 62578
Number of extensions: 233817
Number of successful extensions: 504
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 502
Number of HSP's gapped (non-prelim): 3
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)