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= 024461
         (267 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 =  108 bits (270), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 117/219 (53%), Gaps = 12/219 (5%)

Query: 21  RKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELTLARDIYEHAVLLSVKVEDQDA 80
           RKD+N C + L +LKV L        LF  T +   + + AR+++E+ VL+S++  D ++
Sbjct: 20  RKDWNACKKELLKLKVELAK----QNLFVPTSDK-EKASFARNVFEYGVLVSIQTCDIES 74

Query: 81  FERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNRIAEFHXXXXXX--XXXXXX 138
           F R   Q+ P+Y D+   L PS    ++          +NRIAEFH              
Sbjct: 75  FARYASQVIPFYHDS---LVPSSRMGLVTGLNLLYLLSENRIAEFHTALESVPDKSLFER 131

Query: 139 NPCIKHAVELEQSFMEGAYNRVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYL 198
           +P ++  + LEQ+ MEGA+++V S  ++     + YFM ++   VR+EIA C+EK Y  +
Sbjct: 132 DPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNEIATCAEKVYSEI 191

Query: 199 SIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVFFQK 237
            + +A  +L   + +E  E + EE   W+++DG ++F K
Sbjct: 192 PLSNATSLLYLENTKE-TEKLAEERG-WDIRDGVIYFPK 228


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

 Score = 81.3 bits (199), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/280 (25%), Positives = 126/280 (45%), Gaps = 22/280 (7%)

Query: 3   PKLTEVSQQFDRFKAAMTRKDYNTCTQLLSQLKV-LLTGFRSLPPLFEDTPNAIRELTLA 61
           P L E+++       A    DY  C +LL  +K+ L+     +P L       + +L + 
Sbjct: 2   PSLAELTKSL---SIAFENGDYAACEKLLPPIKIELIKNNLLIPDLSIQNDIYLNDLMIT 58

Query: 62  RDIYEHAVLLSVKVEDQDAFERDFFQLKPYYTDAGKRLPPSPNEYMIXXXXXXXXXVQNR 121
           + I E   L S++  + D+FE  F QLKPYY     +L  S  +  +          QN 
Sbjct: 59  KRILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLSQNN 118

Query: 122 IAEFHXXXX---XXXXXXXXNPCIKHAVELEQSFMEGAYNRVL----SAKQNVPNETYGY 174
             +FH               +  + + ++L++  MEG+Y +      S  QN+    +  
Sbjct: 119 TTKFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNIS--EFDS 176

Query: 175 FMDLLAKTVRDEIAGCSEKAYDYLSIKDAGQMLLFTSDQELLEYVKEEHPEWEMKDGFVF 234
           F D+L   +RDEIA  +E +YD+L + +   +L F +++E  ++  E +  W + +  V+
Sbjct: 177 FTDILKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERN--WPIVNSKVY 234

Query: 235 F-----QKA--KDSAPCKEIPSLQLINQTLSYARELERIV 267
           F     +KA  +D    +E     +I + + YA  +E IV
Sbjct: 235 FNNQSKEKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV 274


>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
 pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
          Length = 715

 Score = 31.2 bits (69), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 15  FKAAMTRKDYNTCTQLLSQLKVLLTGFRSLPPLFEDTPNAIRELT 59
           FK AMT  DY+T    L    +++T +  L  L+   P  + E+ 
Sbjct: 103 FKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVN 147


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

 Score = 28.5 bits (62), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 10/72 (13%)

Query: 159 RVLSAKQNVPNETYGYFMDLLAKTVRDEIAGCSEKAYDYLS--IKDAGQMLLFTSDQELL 216
           R +   Q  PN+     +D+ A  V+ E A   + A+ Y S  + D  Q +      E  
Sbjct: 119 RSVYINQGTPNQLGSMLVDMAANQVKKEQA---KVAFFYSSPTVTDQNQWV-----NEAK 170

Query: 217 EYVKEEHPEWEM 228
           + +++EHP WE+
Sbjct: 171 KKIQQEHPGWEI 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
   0.319    0.135    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,028,332
Number of Sequences: 62578
Number of extensions: 257233
Number of successful extensions: 672
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 664
Number of HSP's gapped (non-prelim): 5
length of query: 267
length of database: 14,973,337
effective HSP length: 97
effective length of query: 170
effective length of database: 8,903,271
effective search space: 1513556070
effective search space used: 1513556070
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: 50 (23.9 bits)