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= psy15259
         (257 letters)

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

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



>pdb|2BF1|A Chain A, Structure Of An Unliganded And Fully-Glycosylated Siv
           Gp120 Envelope Glycoprotein
 pdb|3FUS|A Chain A, Improved Structure Of The Unliganded Simian
           Immunodeficiency Virus Gp120 Core
          Length = 316

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 147 LVAHAIWETSRAKNIEVMKVVAELFREYLGDIPVIPI 183
           L+A+  W      NI +   VAEL+R  LGD  ++ I
Sbjct: 279 LIANIDWTDGNQTNITMSAEVAELYRLELGDYKLVEI 315


  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
   0.319    0.135    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,237,887
Number of Sequences: 62578
Number of extensions: 343625
Number of successful extensions: 699
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 693
Number of HSP's gapped (non-prelim): 11
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)