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= psy7729
         (167 letters)

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

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



>pdb|3LEY|H Chain H, 2f5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal
          Antibody 6a7 In Complex With Hiv-1 Gp41
          Length = 221

 Score = 28.9 bits (63), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 1  MAYRSAYGFNSIIPGFPSYMRVG-DSSHGVYNLRIRNVSLTDDAEFQCQVG 50
          M Y S  GF S  P   S + +  D+S   + L++ +V+  D A + C  G
Sbjct: 49 MGYISYSGFTSYNPSLKSQISITRDTSKNQFFLQLNSVTTEDTATYYCAFG 99


>pdb|3Q6G|L Chain L, Crystal Structure Of Fab Of Rhesus Mab 2.5b Specific For
           Quaternary Neutralizing Epitope Of Hiv-1 Gp120
 pdb|3Q6G|M Chain M, Crystal Structure Of Fab Of Rhesus Mab 2.5b Specific For
           Quaternary Neutralizing Epitope Of Hiv-1 Gp120
          Length = 209

 Score = 27.7 bits (60), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 23  GDSSHGVYNLRIRNVSLTDDAEFQCQV-GPAQYHKPIRANARLTVI 67
           G +S     L I  V   D+A++ CQV   + +H       RLTV+
Sbjct: 62  GSNSGNTATLTISGVEAGDEADYYCQVWDSSSHHMLFGGGTRLTVL 107


>pdb|1ADQ|L Chain L, Crystal Structure Of A Human Igm Rheumatoid Factor Fab In
           Complex With Its Autoantigen Igg Fc
          Length = 213

 Score = 26.9 bits (58), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 2/55 (3%)

Query: 14  PGFPSYMRVGDSSHGVYNLRIRNVSLTDDAEFQCQVGPAQY-HKPIRANARLTVI 67
           PG P     G +S     L I  V   D+A++ CQV  +   H       +LTV+
Sbjct: 54  PGIPERFS-GSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHAVFGGGTKLTVL 107


>pdb|1LIL|A Chain A, Bence Jones Protein Cle, A Lambda Iii Immunoglobulin
           Light- Chain Dimer
 pdb|1LIL|B Chain B, Bence Jones Protein Cle, A Lambda Iii Immunoglobulin
           Light- Chain Dimer
          Length = 212

 Score = 26.2 bits (56), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 19/45 (42%)

Query: 23  GDSSHGVYNLRIRNVSLTDDAEFQCQVGPAQYHKPIRANARLTVI 67
           G SS     L I      D+A++ CQV  +          +LTV+
Sbjct: 62  GSSSGNTATLTISGTQTLDEADYYCQVWDSNASVVFGGGTKLTVL 106


  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
   0.322    0.136    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,673,439
Number of Sequences: 62578
Number of extensions: 74545
Number of successful extensions: 379
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 374
Number of HSP's gapped (non-prelim): 10
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)