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= 018940
         (348 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 = 32.7 bits (73), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 1/102 (0%)

Query: 123 KVETISYCVFAAIFNVGWAATQVAHMSMVNCITLNSTSRVVLTSCRNAFTMVANLSLYAI 182
            +   ++ +     N  W A +VA+   V     N + R V+ + RN      N S    
Sbjct: 164 DISNSAHGIATNTSNYRWTADEVAYAKAVLSAIGNPSLRAVIDTSRNGNGPAGNESCDPS 223

Query: 183 AFIVFSVSTAKTHADLENQYRWIAYSSIFIGC-CFVGIFLSR 223
              + + ST  T   + + + WI       GC    G F+ +
Sbjct: 224 GRAIGTPSTTNTGDPMIDAFLWIKLPGEADGCIAGAGQFVPQ 265


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

 Score = 32.7 bits (73), Expect = 0.34,   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    0.138    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,507,333
Number of Sequences: 62578
Number of extensions: 291154
Number of successful extensions: 670
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: 667
Number of HSP's gapped (non-prelim): 3
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
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: 52 (24.6 bits)