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= 011445
         (485 letters)

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

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



>pdb|3B9K|H Chain H, Crystal Structure Of Cd8alpha-Beta In Complex With Yts
           156.7 Fab
 pdb|3B9K|D Chain D, Crystal Structure Of Cd8alpha-Beta In Complex With Yts
           156.7 Fab
          Length = 214

 Score = 31.6 bits (70), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 2/28 (7%)

Query: 413 CNCIGLSV--DSLRWVKRPSFRGLHWLG 438
           C+  G S+  DS+ WV++P  +GL W+G
Sbjct: 22  CSVSGFSLISDSVHWVRQPPGKGLEWMG 49


>pdb|3IY6|B Chain B, Variable Domains Of The Computer Generated Model (Wam) Of
           Fab E Fitted Into The Cryoem Reconstruction Of The
           Virus- Fab E Complex
          Length = 115

 Score = 30.4 bits (67), Expect = 2.1,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 413 CNCIGLSVDS--LRWVKRPSFRGLHWLGI 439
           C   G S+ S  + WV++P  +GL WLG+
Sbjct: 16  CTVSGFSLSSYHVHWVRQPPGKGLEWLGV 44


>pdb|3VG0|H Chain H, Antibody Fab Fragment
          Length = 223

 Score = 30.4 bits (67), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 413 CNCIGLSV--DSLRWVKRPSFRGLHWLGI 439
           C   G S+  D + W+++P  +GL WLG+
Sbjct: 24  CTISGFSLTDDGVSWIRQPPGKGLEWLGV 52


>pdb|3V6O|C Chain C, Leptin Receptor-Antibody Complex
 pdb|3V6O|D Chain D, Leptin Receptor-Antibody Complex
          Length = 221

 Score = 30.4 bits (67), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 413 CNCIGLSV--DSLRWVKRPSFRGLHWLGI 439
           C   G S+  D + W+++P  +GL WLG+
Sbjct: 23  CTISGFSLTDDGVSWIRQPPGKGLEWLGV 51


>pdb|3VFG|H Chain H, Crystal Structure Of Monoclonal Anitbody 3f8 Fab Fragment
           That Binds To Gd2 Ganglioside
          Length = 219

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 413 CNCIGLSVDS--LRWVKRPSFRGLHWLGI 439
           C   G SV +  + WV++P  +GL WLG+
Sbjct: 22  CTVSGFSVTNYGVHWVRQPPGKGLEWLGV 50


>pdb|3IU4|H Chain H, Anti Neugcgm3 Ganglioside Chimeric Antibody Chp3
          Length = 263

 Score = 29.6 bits (65), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 413 CNCIGLSVD--SLRWVKRPSFRGLHWLGI 439
           C   G S+   S+ WV++P  +GL WLG+
Sbjct: 22  CTVSGFSLSRYSVHWVRQPPGKGLEWLGM 50


>pdb|2ARJ|H Chain H, Cd8alpha-Alpha In Complex With Yts 105.18 Fab
 pdb|2ARJ|B Chain B, Cd8alpha-Alpha In Complex With Yts 105.18 Fab
          Length = 215

 Score = 29.3 bits (64), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 2/28 (7%)

Query: 413 CNCIGLSV--DSLRWVKRPSFRGLHWLG 438
           C   G S+  +S+ WV++P  +GL W+G
Sbjct: 22  CTVSGFSLTSNSVHWVRQPPGKGLEWMG 49


  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
   0.324    0.139    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,523,351
Number of Sequences: 62578
Number of extensions: 458033
Number of successful extensions: 1750
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1743
Number of HSP's gapped (non-prelim): 13
length of query: 485
length of database: 14,973,337
effective HSP length: 103
effective length of query: 382
effective length of database: 8,527,803
effective search space: 3257620746
effective search space used: 3257620746
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 bits)