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= 021436
         (312 letters)

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

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



>pdb|2B0S|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In
           Complex With Mn Peptide
 pdb|2B1A|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In
           Complex With Ug1033 Peptide
 pdb|2B1H|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In
           Complex With Ug29 Peptide
          Length = 215

 Score = 27.7 bits (60), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 25  LSLTCTSQSKNLKNEIYAHCLDLPSLSSFLHFTYDASNRSLSIAFVAAPAKSGGWIAWAI 84
           +S++C+  S N++N        LP  +  L   Y   +RS  I    + +KSG   + AI
Sbjct: 18  ISISCSGTSSNVENNYVYWYQHLPGTAPKL-LIYRNDHRSSGIPDRFSASKSGTSASLAI 76

Query: 85  NPTAPGMAGSQALVAYKDSKG 105
           +   P   G     A+ DS+G
Sbjct: 77  SGLRPEDEGDYYCAAWDDSRG 97


  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
   0.318    0.132    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,651,966
Number of Sequences: 62578
Number of extensions: 335413
Number of successful extensions: 793
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 793
Number of HSP's gapped (non-prelim): 2
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)