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= 034247
         (100 letters)

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

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



>pdb|2QAD|A Chain A, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
           With Hiv-1 Yu2 Gp120 And Cd4
 pdb|2QAD|E Chain E, Structure Of Tyrosine-Sulfated 412d Antibody Complexed
           With Hiv-1 Yu2 Gp120 And Cd4
          Length = 322

 Score = 25.8 bits (55), Expect = 5.8,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 16  SSDRNVVPIAPLQFESPVGQLLAQILQTHPHLLPAAIDQQLENIQIDKNVQREDTSQDLL 75
           ++ R  + I P +     G+++  I Q H +L     +  LE I I K  ++   ++ ++
Sbjct: 140 NNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAI-KLKEQFGNNKTII 198

Query: 76  YQPYGGG 82
           + P  GG
Sbjct: 199 FNPSSGG 205


>pdb|3HI1|G Chain G, Structure Of Hiv-1 Gp120 (Core With V3) In Complex With
           Cd4-Binding- Site Antibody F105
 pdb|3HI1|J Chain J, Structure Of Hiv-1 Gp120 (Core With V3) In Complex With
           Cd4-Binding- Site Antibody F105
          Length = 321

 Score = 25.8 bits (55), Expect = 5.8,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 16  SSDRNVVPIAPLQFESPVGQLLAQILQTHPHLLPAAIDQQLENIQIDKNVQREDTSQDLL 75
           ++ R  + I P +     G+++  I Q H +L     +  LE I I K  ++   ++ ++
Sbjct: 139 NNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAI-KLKEQFGNNKTII 197

Query: 76  YQPYGGG 82
           + P  GG
Sbjct: 198 FNPSSGG 204


  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
   0.316    0.133    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,882,303
Number of Sequences: 62578
Number of extensions: 98413
Number of successful extensions: 225
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 224
Number of HSP's gapped (non-prelim): 5
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)