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= psy2033
         (124 letters)

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

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



>pdb|1CKS|A Chain A, Human Ckshs2 Atomic Structure: A Role For Its Hexameric
          Assembly In Cell Cycle Control
 pdb|1CKS|B Chain B, Human Ckshs2 Atomic Structure: A Role For Its Hexameric
          Assembly In Cell Cycle Control
 pdb|1CKS|C Chain C, Human Ckshs2 Atomic Structure: A Role For Its Hexameric
          Assembly In Cell Cycle Control
          Length = 79

 Score = 27.3 bits (59), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 15/34 (44%)

Query: 21 PESLSGVVPAMHYGYVEGWFSKVAQASLGWLLLM 54
          P  LS  VP  H    E W     Q SLGW+  M
Sbjct: 25 PRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYM 58


>pdb|3HUR|A Chain A, Crystal Structure Of Alanine Racemase From Oenococcus Oeni
          Length = 395

 Score = 27.3 bits (59), Expect = 2.3,   Method: Composition-based stats.
 Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 3/38 (7%)

Query: 11  LGAGQTEQQPPESLSGVVPAMHYGYVEGWFSKVAQASL 48
           L  G +E+ P +   G V  + +GY +GW  ++ ++S+
Sbjct: 269 LSYGASERMPED---GYVATLPFGYNDGWLRRMQKSSV 303


>pdb|3TMP|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba In
          Complex With Ubiquitin Aldehyde
 pdb|3TMP|C Chain C, The Catalytic Domain Of Human Deubiquitinase Duba In
          Complex With Ubiquitin Aldehyde
 pdb|3TMP|E Chain E, The Catalytic Domain Of Human Deubiquitinase Duba In
          Complex With Ubiquitin Aldehyde
 pdb|3TMP|G Chain G, The Catalytic Domain Of Human Deubiquitinase Duba In
          Complex With Ubiquitin Aldehyde
          Length = 184

 Score = 26.2 bits (56), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 9  SHLGAGQTEQQPPESLSGVVPAMHYGYVEG---WFSKVAQASLGWLL 52
          SH+GAG   +   E+ +  + AM    VE    WF K  +   G+++
Sbjct: 2  SHMGAGYNXEDEYEAAAARIEAMDPATVEQQEHWFEKALRDKKGFII 48


>pdb|2WUU|A Chain A, Structure Of N-Myristoyltransferase From L. Donovani
          Length = 421

 Score = 25.4 bits (54), Expect = 7.9,   Method: Composition-based stats.
 Identities = 8/20 (40%), Positives = 16/20 (80%)

Query: 92  VVSAAFVHYHGITEMAMYRL 111
           +++AA+VHY+  T M +++L
Sbjct: 340 ILNAAYVHYYAATSMPLHQL 359


  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    0.140    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,035,901
Number of Sequences: 62578
Number of extensions: 148820
Number of successful extensions: 197
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 195
Number of HSP's gapped (non-prelim): 4
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)