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= 028424
         (209 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 = 94.0 bits (232), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 96/177 (54%), Gaps = 7/177 (3%)

Query: 5   DIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRI 64
           +++E+ VL+S++  D ++F R   Q+ P+Y D+   L PS    ++          +NRI
Sbjct: 57  NVFEYGVLVSIQTCDIESFARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRI 113

Query: 65  AEFHXXXXXX--XXXXXXNPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLA 122
           AEFH              +P ++  + LEQ+ MEGA+++V S  ++     + YFM ++ 
Sbjct: 114 AEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVM 173

Query: 123 KTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK 179
             VR+EIA C+EK Y  + + +A  +L   + +E  E + EE   W+++DG ++F K
Sbjct: 174 SMVRNEIATCAEKVYSEIPLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFPK 228


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

 Score = 70.9 bits (172), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 58/223 (26%), Positives = 103/223 (46%), Gaps = 18/223 (8%)

Query: 1   MVSGDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXV 60
           M++  I E   L S++  + D+FE  F QLKPYY     +L  S  +  +          
Sbjct: 56  MITKRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLS 115

Query: 61  QNRIAEFHXXXX---XXXXXXXXNPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNET 113
           QN   +FH               +  + + ++L++  MEG+Y +      S  QN+    
Sbjct: 116 QNNTTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--E 173

Query: 114 YGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDG 173
           +  F D+L   +RDEIA  +E +YD+L + +   +L F +++E  ++  E +  W + + 
Sbjct: 174 FDSFTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNS 231

Query: 174 FVFF-----QKA--KDSAPCKEIPSLQLINQTLSYARELERIV 209
            V+F     +KA  +D    +E     +I + + YA  +E IV
Sbjct: 232 KVYFNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV 274


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

 Score = 28.5 bits (62), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 101 RVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEY 160
           R +   Q  PN+     +D+ A  V+ E A  +   Y   ++ D  Q +      E  + 
Sbjct: 119 RSVYINQGTPNQLGSMLVDMAANQVKKEQAKVAF-FYSSPTVTDQNQWV-----NEAKKK 172

Query: 161 VKEEHPEWEM 170
           +++EHP WE+
Sbjct: 173 IQQEHPGWEI 182


  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    0.135    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,587,070
Number of Sequences: 62578
Number of extensions: 200456
Number of successful extensions: 497
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 491
Number of HSP's gapped (non-prelim): 3
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)