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= 031345
         (161 letters)

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

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



>pdb|4B0Z|A Chain A, Crystal Structure Of S. Pombe Rpn12
 pdb|4B0Z|B Chain B, Crystal Structure Of S. Pombe Rpn12
          Length = 229

 Score = 73.9 bits (180), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 40/121 (33%), Positives = 68/121 (56%), Gaps = 4/121 (3%)

Query: 13  QNRIAEFHXXXXXX--XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFM 70
           +NRIAEFH              +P ++  + LEQ+ MEGA+++V S  ++     + YFM
Sbjct: 110 ENRIAEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFM 169

Query: 71  DLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQ 130
            ++   VR+EIA C+EK Y  + + +A  +L   + +E  E + EE   W+++DG ++F 
Sbjct: 170 KIVMSMVRNEIATCAEKVYSEIPLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFP 227

Query: 131 K 131
           K
Sbjct: 228 K 228


>pdb|4B4T|T Chain T, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 274

 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 37/140 (26%), Positives = 72/140 (51%), Gaps = 15/140 (10%)

Query: 33  NPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKA 88
           +  + + ++L++  MEG+Y +      S  QN+    +  F D+L   +RDEIA  +E +
Sbjct: 139 DSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--EFDSFTDILKSAIRDEIAKNTELS 196

Query: 89  YDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFF-----QKA--KDSAPCKEI 141
           YD+L + +   +L F +++E  ++  E +  W + +  V+F     +KA  +D    +E 
Sbjct: 197 YDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNSKVYFNNQSKEKADYEDEMMHEED 254

Query: 142 PSLQLINQTLSYARELERIV 161
               +I + + YA  +E IV
Sbjct: 255 QKTNIIEKAMDYAISIENIV 274


>pdb|3T95|A Chain A, Crystal Structure Of Lsrb From Yersinia Pestis Complexed
           With Autoinducer-2
          Length = 335

 Score = 28.1 bits (61), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 53  RVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEY 112
           R +   Q  PN+     +D+ A  V+ E A  +   Y   ++ D  Q +      E  + 
Sbjct: 119 RSVYINQGTPNQLGSMLVDMAANQVKKEQAKVAF-FYSSPTVTDQNQWV-----NEAKKK 172

Query: 113 VKEEHPEWEM 122
           +++EHP WE+
Sbjct: 173 IQQEHPGWEI 182


>pdb|3Q91|A Chain A, Crystal Structure Of Human Uridine Diphosphate Glucose
           Pyrophosphatase (Nudt14)
 pdb|3Q91|C Chain C, Crystal Structure Of Human Uridine Diphosphate Glucose
           Pyrophosphatase (Nudt14)
 pdb|3Q91|B Chain B, Crystal Structure Of Human Uridine Diphosphate Glucose
           Pyrophosphatase (Nudt14)
 pdb|3Q91|D Chain D, Crystal Structure Of Human Uridine Diphosphate Glucose
           Pyrophosphatase (Nudt14)
          Length = 218

 Score = 26.6 bits (57), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 11/34 (32%), Positives = 21/34 (61%)

Query: 85  SEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHP 118
           ++K++D++   D+  +LLF S +  L  VK+  P
Sbjct: 26  AQKSWDFMKTHDSVTVLLFNSSRRSLVLVKQFRP 59


  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
   0.318    0.134    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,001,801
Number of Sequences: 62578
Number of extensions: 149325
Number of successful extensions: 395
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 8
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)