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= 014255
         (428 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 = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 85/346 (24%), Positives = 169/346 (48%), Gaps = 30/346 (8%)

Query: 59  QTVKLYYRLGKYKEMMDAYREMLTYIKSAVTRNYSEKCINNIMD-FVSGSASQNFSLLRE 117
           Q  +LY + GK KE+ D  +    ++ S++++  + K + +++D F+   A     +   
Sbjct: 24  QQGELYKQEGKAKELADLIKVTRPFL-SSISKAKAAKLVRSLVDMFLDMDAGTGIEV--- 79

Query: 118 FYQTTLKALEEAKNE-RLWFKTNL--KLCKIWFDMGEYGRM----SKILKELHKSCQRED 170
             Q     +E AK E R + + +L  +L  ++FD   Y       +++L+EL K      
Sbjct: 80  --QLCKDCIEWAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKK------ 131

Query: 171 GTDDQKKGSQLLEVYAIEIQMYTETXXXXXXXXXXXXXXXXXSAI-PHPRIMGIIRECGG 229
             DD+   + L+EV  +E + Y                    +AI   P++ G +    G
Sbjct: 132 -LDDK---NLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALDLQSG 187

Query: 230 KMHMA-ERQWADAATDFFEAFKNYDEAGNQRRIQCLKYLVLANMLM--ESEVNPF-DGQE 285
            +H A ER +  A + F+EAF+ +D   + + +  LKY++L  +++    +VN    G+ 
Sbjct: 188 ILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKIMLGQSDDVNQLVSGKL 247

Query: 286 AKPYKNDPEILAMTNLIAAYQRNEIIEFEKILKSNRKTIMDDPFIRNYIEDLLKNVRTQV 345
           A  Y    +I AM ++  A  +  + +F+  LK  +K + +D  ++ ++  L   +  Q 
Sbjct: 248 AITYSG-RDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYDTMLEQN 306

Query: 346 LLKLIKPYTRIRIPFISKELNVPEKDVEQLLVSLILDNRIDGHIDQ 391
           L ++I+PY+R+++  +++ + +P   VE+ L  +ILD +  G +DQ
Sbjct: 307 LCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQ 352


>pdb|4B4T|Q Chain Q, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 434

 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/281 (23%), Positives = 127/281 (45%), Gaps = 17/281 (6%)

Query: 124 KALEEAKNE-RLWFKTNL--KLCKIWFDMGEYGRMSKILKELHKSCQREDGTDDQKKGSQ 180
           K++E AK E R++ K +L  KL  + +   +Y     ++ +L +  ++ D          
Sbjct: 120 KSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDD------KPS 173

Query: 181 LLEVYAIEIQMYTETXXXXXXXXXXXXXXXXXSAIPHP-RIMGIIRECGGKMHMAERQWA 239
           L++V+ +E ++Y +                  ++I  P + +  +    G +H  ++ + 
Sbjct: 174 LVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYK 233

Query: 240 DAATDFFEAFKNYDEAGN----QRRIQCLKYLVLANM---LMESEVNPFDGQEAKPYKND 292
            A + FFE+F++Y         ++  Q LKY++L+ +   L++   N  + +  K     
Sbjct: 234 TAFSYFFESFESYHNLTTHNSYEKACQVLKYMLLSKIMLNLIDDVKNILNAKYTKETYQS 293

Query: 293 PEILAMTNLIAAYQRNEIIEFEKILKSNRKTIMDDPFIRNYIEDLLKNVRTQVLLKLIKP 352
             I AM  +  AY    +++F   LK   K +M D   R++   L   +    L K+I+P
Sbjct: 294 RGIDAMKAVAEAYNNRSLLDFNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEP 353

Query: 353 YTRIRIPFISKELNVPEKDVEQLLVSLILDNRIDGHIDQVN 393
           +  + I  ISK + +  + VE  L  +ILD    G +DQ N
Sbjct: 354 FECVEISHISKIIGLDTQQVEGKLSQMILDKIFYGVLDQGN 394


>pdb|4B4T|O Chain O, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 393

 Score = 32.3 bits (72), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 11/69 (15%)

Query: 361 ISKELNVPEKDVEQLLVSLILDNRIDGHIDQVNRLLE---------RGDRSKGMKKYTAI 411
           ISK  ++P+ +VE L++  I    + G IDQVN L+           GD+   MK     
Sbjct: 313 ISKATHLPKDNVEHLVMRAISLGLLKGSIDQVNELVTISWVQPRIISGDQITKMKDRLV- 371

Query: 412 DKWNSQLRK 420
            +WN Q+ K
Sbjct: 372 -EWNDQVEK 379


  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
   0.321    0.136    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,921,559
Number of Sequences: 62578
Number of extensions: 469297
Number of successful extensions: 1219
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1215
Number of HSP's gapped (non-prelim): 10
length of query: 428
length of database: 14,973,337
effective HSP length: 102
effective length of query: 326
effective length of database: 8,590,381
effective search space: 2800464206
effective search space used: 2800464206
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: 53 (25.0 bits)