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= 021040
         (318 letters)

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

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



>pdb|3RPT|X Chain X, Crystal Structure Of The Anti-Hiv B12 Scaffold Protein
 pdb|3RPT|A Chain A, Crystal Structure Of The Anti-Hiv B12 Scaffold Protein
          Length = 282

 Score = 33.1 bits (74), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 21/85 (24%), Positives = 33/85 (38%), Gaps = 1/85 (1%)

Query: 140 WAATQVAHMSMVNCITLNSTSRVVLTSCRNAFTMVANLSLYAIAFIVFSVSTAKTHADLE 199
           W A +VA+   V     N + R V+ + RN      N S       + + ST  T   + 
Sbjct: 181 WTADEVAYAKAVLSAIGNPSLRAVIDTSRNGNGPAGNESCDPSGRAIGTPSTTNTGDPMI 240

Query: 200 NQYRWIAYSSIFIGC-CFVGIFLSR 223
           + + WI       GC    G F+ +
Sbjct: 241 DAFLWIKLPGEADGCIAGAGQFVPQ 265


>pdb|3RU8|X Chain X, Structure Of An Hiv Epitope Scaffold In Complex With
           Neutralizing Antibody B12 Fab
          Length = 282

 Score = 33.1 bits (74), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 137 NVGWAATQVAHMSMVNCITLNSTSRVVLTSCRNAFTMVANLSLYAIAFIVFSVSTAKTHA 196
           N  W A +VA+   V     N + R V+ + RN      N S       + + ST  T  
Sbjct: 178 NYRWTADEVAYAKAVLSAIGNPSLRAVIDTSRNGNGPAGNESCDPSGRAIGTPSTTNTGD 237

Query: 197 DLENQYRWIAYSSIFIGC-CFVGIFLSR 223
            + + + WI       GC    G F+ +
Sbjct: 238 PMIDAFLWIKLPGEADGCIAGAGQFVPQ 265


  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
   0.329    0.137    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,466,554
Number of Sequences: 62578
Number of extensions: 249894
Number of successful extensions: 524
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 521
Number of HSP's gapped (non-prelim): 3
length of query: 318
length of database: 14,973,337
effective HSP length: 99
effective length of query: 219
effective length of database: 8,778,115
effective search space: 1922407185
effective search space used: 1922407185
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 bits)