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= 040208
         (117 letters)

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

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



>pdb|1VSY|5 Chain 5, Proteasome Activator Complex
 pdb|1VSY|8 Chain 8, Proteasome Activator Complex
 pdb|3L5Q|6 Chain 6, Proteasome Activator Complex
 pdb|3L5Q|8 Chain 8, Proteasome Activator Complex
          Length = 997

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 3/36 (8%)

Query: 35  DLVADEKIPFLACLASALKEHSFFPYEPPAGTKRFQ 70
           D+V   KIP   C+ S   + +F P  PP GT   Q
Sbjct: 242 DIVIGIKIPSSVCVIS---DQAFLPLAPPDGTINLQ 274


>pdb|2WV0|A Chain A, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|B Chain B, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|C Chain C, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|D Chain D, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|E Chain E, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|F Chain F, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|G Chain G, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|H Chain H, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|I Chain I, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
 pdb|2WV0|J Chain J, Crystal Structure Of The Gntr-Hutc Family Member Yvoa From
           Bacillus Subtilis
          Length = 243

 Score = 26.2 bits (56), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 54  EHSFFPYEPPA--GTKRFQNLIADFMKMYHHIPLNADCQSLQPKVINIDE 101
           E S  P+E         FQ+ I D ++ Y+ IP++   Q L+P     +E
Sbjct: 145 ESSHIPFELAGELNESHFQSSIYDHIERYNSIPISRAKQELEPSAATTEE 194


>pdb|3FKK|A Chain A, Structure Of L-2-Keto-3-Deoxyarabonate Dehydratase
 pdb|3FKK|B Chain B, Structure Of L-2-Keto-3-Deoxyarabonate Dehydratase
          Length = 309

 Score = 25.8 bits (55), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 10/31 (32%), Positives = 18/31 (58%)

Query: 43  PFLACLASALKEHSFFPYEPPAGTKRFQNLI 73
           PFLA +A  +++ ++F  E P    + + LI
Sbjct: 155 PFLARMAREIEQVAYFKIETPGAANKLRELI 185


>pdb|3FKR|A Chain A, Structure Of L-2-Keto-3-Deoxyarabonate Dehydratase Complex
           With Pyruvate
 pdb|3FKR|B Chain B, Structure Of L-2-Keto-3-Deoxyarabonate Dehydratase Complex
           With Pyruvate
          Length = 309

 Score = 25.8 bits (55), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 10/31 (32%), Positives = 18/31 (58%)

Query: 43  PFLACLASALKEHSFFPYEPPAGTKRFQNLI 73
           PFLA +A  +++ ++F  E P    + + LI
Sbjct: 155 PFLARMAREIEQVAYFXIETPGAANKLRELI 185


>pdb|1VIO|A Chain A, Crystal Structure Of Pseudouridylate Synthase
 pdb|1VIO|B Chain B, Crystal Structure Of Pseudouridylate Synthase
          Length = 243

 Score = 25.4 bits (54), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 12/56 (21%)

Query: 10 VKKIFEFLKNGFYEISSSLDLYFEDDLVADEKIPFLACLASALKEHSFFPYEPPAG 65
          VK   E +K+G  +IS   ++YFED+L+            + ++E  +F    P G
Sbjct: 29 VKINGEIVKSGSVQISQEDEIYFEDELL------------TWIEEGQYFMLNKPQG 72


  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
   0.319    0.136    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,535,664
Number of Sequences: 62578
Number of extensions: 127074
Number of successful extensions: 276
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 270
Number of HSP's gapped (non-prelim): 10
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)