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= 045719
         (384 letters)

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

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



>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 = 30.4 bits (67), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 196 IKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYS 240
           IK +  DG C FRA+AD +   ++    VRK  ++ L  N +++S
Sbjct: 48  IKQMKEDGACLFRAVADQVYGDQDMHEVVRKHCMDYLMKNADYFS 92


>pdb|2D2R|A Chain A, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase
 pdb|2D2R|B Chain B, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase
 pdb|2DTN|A Chain A, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase Complexed With Pyrophosphate
 pdb|2DTN|B Chain B, Crystal Structure Of Helicobacter Pylori Undecaprenyl
           Pyrophosphate Synthase Complexed With Pyrophosphate
          Length = 245

 Score = 30.0 bits (66), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 9/82 (10%)

Query: 189 LQSYIHHIKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYSH----LYG 244
           L+ Y+   +    D N  FRAI DL GF +       +D + +L  +  H+      L  
Sbjct: 87  LKKYLKDERSTYLDNNIRFRAIGDLEGFSKE-----LRDTILQLENDTRHFKDFTQVLAL 141

Query: 245 TYERVNELIHAISYFENCPGSD 266
            Y   NEL  A       P S+
Sbjct: 142 NYGSKNELSRAFKSLLESPPSN 163


>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
          Length = 185

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 24/45 (53%)

Query: 196 IKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYS 240
           IK    DG C FRA+AD +   ++    VRK   + L  N +++S
Sbjct: 61  IKQXKEDGACLFRAVADQVYGDQDXHEVVRKHCXDYLXKNADYFS 105


>pdb|3TMO|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba
          Length = 184

 Score = 29.3 bits (64), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 24/45 (53%)

Query: 196 IKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYS 240
           IK    DG C FRA+AD +   ++    VRK   + L  N +++S
Sbjct: 48  IKQXKEDGACLFRAVADQVYGDQDXHEVVRKHCXDYLXKNADYFS 92


>pdb|3LRF|A Chain A, Crystal Structure Of Beta-Ketoacyl Synthase From Brucella
           Melitensis
 pdb|3MQD|A Chain A, Crystal Structure Of Beta-Ketoacyl Synthase From Brucella
           Melitensis With Fol 0758, (1-Methyl-1h-Indazol-3-Yl)
           Methanol
 pdb|3U0E|A Chain A, Crystal Structure Of Beta-Ketoacyl Synthase From Brucella
           Melitensis In Complex With Fragment 9320
          Length = 428

 Score = 28.5 bits (62), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 13  GIDVSVCGCTIRSTHGLPCAHEIVEYKRESRPIPLECIDSHW 54
           GI+ S+      S H +  A+E+++Y ++ R     C D  W
Sbjct: 173 GINYSISSACATSNHCIGNAYEMIQYGKQDRMFAGGCEDLDW 214


>pdb|3U0F|A Chain A, The Structure Of Beta-Ketoacyl Synthase From Brucella
           Melitensis Bound To The Fragment 7-Hydroxycoumarin
          Length = 411

 Score = 28.1 bits (61), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 13  GIDVSVCGCTIRSTHGLPCAHEIVEYKRESRPIPLECIDSHW 54
           GI+ S+      S H +  A+E+++Y ++ R     C D  W
Sbjct: 156 GINYSISSACATSNHCIGNAYEMIQYGKQDRMFAGGCEDLDW 197


  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
   0.320    0.136    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,506,575
Number of Sequences: 62578
Number of extensions: 534439
Number of successful extensions: 1042
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1036
Number of HSP's gapped (non-prelim): 16
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
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: 52 (24.6 bits)