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= 047869
         (2233 letters)

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

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



>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
           Gd(3+) Complex
 pdb|3TXN|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
           Native Data
          Length = 394

 Score = 34.7 bits (78), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 45/160 (28%), Positives = 71/160 (44%), Gaps = 29/160 (18%)

Query: 78  GFQSWTCDQVHAVTSLGHVI-------------ASASRSLAVEQAGPVIVAVM------- 117
           GF S   D V A+TSL +++                S  LA+  +G  I A+        
Sbjct: 210 GFDS--VDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGKLAITYSGRDIDAMKSVAEASH 267

Query: 118 -QELLEFAVCYLERSEFDNDDFSVQNHMGQLLEIVLIGGTDKVIE---QVQLYPVNSLVQ 173
            + L +F     E  +   +D  VQ H+G L + +L     ++IE   +VQ+  V   +Q
Sbjct: 268 KRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQ 327

Query: 174 L-LPIVSTDCDDIVLDDQINCCL-QG-GVTCSREEKPLDR 210
           L +P V      ++LD + +  L QG GV    EE P+D+
Sbjct: 328 LPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEETPVDK 367


>pdb|1QO0|D Chain D, Amide Receptor Of The Amidase Operon Of Pseudomonas
            Aeruginosa (Amic) Complexed With The Positive Regulator
            Amir.
 pdb|1QO0|E Chain E, Amide Receptor Of The Amidase Operon Of Pseudomonas
            Aeruginosa (Amic) Complexed With The Positive Regulator
            Amir
          Length = 196

 Score = 32.7 bits (73), Expect = 2.2,   Method: Composition-based stats.
 Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 1886 DCQVLTLNPRGEVTDRLAIELALQGAYIRRVDWVP 1920
            + QVL LNP GEV+D L ++L   G  +R+  W P
Sbjct: 12   ELQVLVLNPPGEVSDALVLQLIRIGCSVRQC-WPP 45


  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    0.135    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 58,904,991
Number of Sequences: 62578
Number of extensions: 2277116
Number of successful extensions: 4654
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 4653
Number of HSP's gapped (non-prelim): 2
length of query: 2233
length of database: 14,973,337
effective HSP length: 114
effective length of query: 2119
effective length of database: 7,839,445
effective search space: 16611783955
effective search space used: 16611783955
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: 59 (27.3 bits)