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= 045479
         (482 letters)

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

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



>pdb|3REA|B Chain B, Hiv-1 Nef Protein In Complex With Engineered Hck-Sh3
           Domain
 pdb|3REA|D Chain D, Hiv-1 Nef Protein In Complex With Engineered Hck-Sh3
           Domain
          Length = 61

 Score = 30.0 bits (66), Expect = 3.2,   Method: Composition-based stats.
 Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 4/32 (12%)

Query: 449 DDGSFELGDHW----ENGELWTASSVLTNKDG 476
           DD SF+ GD      E+GE W A S+ T K+G
Sbjct: 18  DDLSFQKGDQMVVLEESGEWWKARSLATRKEG 49


>pdb|3REB|B Chain B, Hiv-1 Nef Protein In Complex With Engineered Hck-Sh3
           Domain
 pdb|3REB|D Chain D, Hiv-1 Nef Protein In Complex With Engineered Hck-Sh3
           Domain
          Length = 90

 Score = 29.6 bits (65), Expect = 4.3,   Method: Composition-based stats.
 Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 4/32 (12%)

Query: 449 DDGSFELGDHW----ENGELWTASSVLTNKDG 476
           DD SF+ GD      E+GE W A S+ T K+G
Sbjct: 18  DDLSFQKGDQMVVLEESGEWWKARSLATRKEG 49


>pdb|1W1F|A Chain A, Sh3 Domain Of Human Lyn Tyrosine Kinase
 pdb|1WA7|A Chain A, Sh3 Domain Of Human Lyn Tyrosine Kinase In Complex With A
           Herpesviral Ligand
          Length = 65

 Score = 29.3 bits (64), Expect = 4.8,   Method: Composition-based stats.
 Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 4/32 (12%)

Query: 449 DDGSFELGDHW----ENGELWTASSVLTNKDG 476
           DD SF+ G+      E+GE W A S+LT K+G
Sbjct: 22  DDLSFKKGEKMKVLEEHGEWWKAKSLLTKKEG 53


>pdb|3RBB|B Chain B, Hiv-1 Nef Protein In Complex With Engineered Hck Sh3
           Domain
 pdb|3RBB|D Chain D, Hiv-1 Nef Protein In Complex With Engineered Hck Sh3
           Domain
          Length = 61

 Score = 28.9 bits (63), Expect = 5.9,   Method: Composition-based stats.
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 6/39 (15%)

Query: 444 DYH--FDDDGSFELGDHW----ENGELWTASSVLTNKDG 476
           DY+  F  D SF+ GD      E+GE W A S+ T K+G
Sbjct: 11  DYYSPFSWDLSFQKGDQMVVLEESGEWWKARSLATRKEG 49


>pdb|1ML4|A Chain A, The Pala-Liganded Aspartate Transcarbamoylase Catalytic
           Subunit From Pyrococcus Abyssi
          Length = 308

 Score = 28.5 bits (62), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 19/79 (24%)

Query: 319 QTLIDHLTHFRKDFGLSNNLR------------------AMILRHPELFYVSPKGIRNSV 360
           QTL+D  T  +K+FG  + L+                  A+     EL+ +SP+ +R   
Sbjct: 138 QTLLDLYT-IKKEFGRIDGLKIGLLGDLKYGRTVHSLAEALTFYDVELYLISPELLRMPR 196

Query: 361 QLVEEFDEKGVLLKRDETL 379
            +VEE  EKG+ +    TL
Sbjct: 197 HIVEELREKGMKVVETTTL 215


  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
   0.321    0.135    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,583,935
Number of Sequences: 62578
Number of extensions: 390704
Number of successful extensions: 856
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 855
Number of HSP's gapped (non-prelim): 6
length of query: 482
length of database: 14,973,337
effective HSP length: 103
effective length of query: 379
effective length of database: 8,527,803
effective search space: 3232037337
effective search space used: 3232037337
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)