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= 043891
         (200 letters)

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

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



>pdb|3OLM|A Chain A, Structure And Function Of A Ubiquitin Binding Site
          Within The Catalytic Domain Of A Hect Ubiquitin Ligase
          Length = 429

 Score = 27.7 bits (60), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 3  NTSAVTASLDNPASQLKNETSRPSRVIYFRIDVALRIL 40
          +   + +SLD    Q K +  R  +VIYFR   ALRIL
Sbjct: 36 DDPRLPSSLDQNVPQYKRDFRR--KVIYFRSQPALRIL 71


>pdb|1YGP|A Chain A, Phosphorylated Form Of Yeast Glycogen Phosphorylase With
           Phosphate Bound In The Active Site.
 pdb|1YGP|B Chain B, Phosphorylated Form Of Yeast Glycogen Phosphorylase With
           Phosphate Bound In The Active Site
          Length = 879

 Score = 27.7 bits (60), Expect = 4.5,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 7/42 (16%)

Query: 150 SHAGWNK-------QANAGYDKFIKHTATAIALSIFAVTDLV 184
           S A WNK       +A    D+FI H  T +A S++   D+V
Sbjct: 26  SRALWNKHQVKKFNKAEDFQDRFIDHVETTLARSLYNCDDMV 67


  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
   0.326    0.135    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,919,880
Number of Sequences: 62578
Number of extensions: 109213
Number of successful extensions: 211
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 211
Number of HSP's gapped (non-prelim): 4
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)