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= psy14516
         (76 letters)

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

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



>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain
          Length = 109

 Score = 72.4 bits (176), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 31/53 (58%), Positives = 37/53 (69%)

Query: 20 TPLADCPHTPLVAPVPQSGVDVKAPCVDCASVAENWVCLICYQVRCGRYIEEH 72
          +PL  CPH   V P+P +G+DV  PC DC ++ ENWVCL CYQV CGRYI  H
Sbjct: 2  SPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGH 54


>pdb|3GV4|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain And
          Ubiquitin C-Terminal Peptide Rlrgg
 pdb|3PHD|A Chain A, Crystal Structure Of Human Hdac6 In Complex With
          Ubiquitin
 pdb|3PHD|B Chain B, Crystal Structure Of Human Hdac6 In Complex With
          Ubiquitin
 pdb|3PHD|C Chain C, Crystal Structure Of Human Hdac6 In Complex With
          Ubiquitin
 pdb|3PHD|D Chain D, Crystal Structure Of Human Hdac6 In Complex With
          Ubiquitin
          Length = 107

 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 31/52 (59%), Positives = 36/52 (69%)

Query: 21 PLADCPHTPLVAPVPQSGVDVKAPCVDCASVAENWVCLICYQVRCGRYIEEH 72
          PL  CPH   V P+P +G+DV  PC DC ++ ENWVCL CYQV CGRYI  H
Sbjct: 1  PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGH 52


  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
   0.322    0.136    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,266,246
Number of Sequences: 62578
Number of extensions: 71758
Number of successful extensions: 127
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 125
Number of HSP's gapped (non-prelim): 2
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)