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= 025802
         (248 letters)

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

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



>pdb|3KLR|A Chain A, Bovine H-Protein At 0.88 Angstrom Resolution
          Length = 125

 Score = 32.3 bits (72), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 12/85 (14%)

Query: 30  LNKQQPQIGPDPICNPARFKTSGSSYSPLNDPSPNWSNRPPKET--IMLDGCDYQHWLIV 87
           LNKQ+     + +      K +   YSPL+       N+   E   ++   C    WLI 
Sbjct: 46  LNKQEEFGALESV------KAASELYSPLSGEVTE-INKALAENPGLVNKSCYEDGWLIK 98

Query: 88  MEFPNPSELSE---EEMINAYVKTL 109
           M F NPSEL E   EE    Y+K++
Sbjct: 99  MTFSNPSELDELMSEEAYEKYIKSI 123


>pdb|2EDG|A Chain A, Solution Structure Of The Gcv_h Domain From Mouse Glycine
          Length = 130

 Score = 28.5 bits (62), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 3/34 (8%)

Query: 79  CDYQHWLIVMEFPNPSELSE---EEMINAYVKTL 109
           C    WLI M   +PSEL E   EE    YVK++
Sbjct: 95  CYEDGWLIKMTLSDPSELDELMSEEAYEKYVKSI 128


  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
   0.313    0.130    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,615,155
Number of Sequences: 62578
Number of extensions: 308238
Number of successful extensions: 391
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 388
Number of HSP's gapped (non-prelim): 9
length of query: 248
length of database: 14,973,337
effective HSP length: 96
effective length of query: 152
effective length of database: 8,965,849
effective search space: 1362809048
effective search space used: 1362809048
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)