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= 005098
         (714 letters)

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

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



>pdb|4B4T|N Chain N, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 945

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 97/425 (22%), Positives = 183/425 (43%), Gaps = 36/425 (8%)

Query: 192 AATFVNAFVNAGFGQDKLMTVPSDASSGGSSGNWLFKNKEHGKMSAAASLGMILLWDVDS 251
           A +  N F++AG          +D S   ++  WL K +   K +A ASLG+I   ++  
Sbjct: 331 AVSVANGFMHAG---------TTDNSFIKANLPWLGKAQNWAKFTATASLGVIHKGNLLE 381

Query: 252 GLAQIDKYF---HSTDNHVIAGALLGVGIVNCGIRNDCDPALALL----SEYVGREDACI 304
           G   +  Y     ++   +  G+L G+G++  G   D    L  +    S   G ED  +
Sbjct: 382 GKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDV 441

Query: 305 RI-GAIMGLGISYAGTQNDQIRHKLSTIL-NDAKSPLDVIAFSAISLGLIYVGSCNEEVA 362
            + GA +G+G++  G+ N ++   L  +L ND+ +  +    +A+ +GL  +G+   E  
Sbjct: 442 LLHGASLGIGLAAMGSANIEVYEALKEVLYNDSATSGEA---AALGMGLCMLGTGKPEA- 497

Query: 363 QAIIFALMDRSESELGEPXXXXXXXXXXXXXXXKQESVEATAEVSKTFNEKIRKYCDMTL 422
              I  +   S+                     +QE  +         +E + +Y     
Sbjct: 498 ---IHDMFTYSQETQHGNITRGLAVGLALINYGRQELADDLITKMLASDESLLRYGGAFT 554

Query: 423 LSCAYAGTGNVLKVQNLLGHCAQHHEKGEAYQGPAVLGIAMVAMAEELGLEMAIRSLEHL 482
           ++ AYAGTGN   V+ LL H A      +  +  AV+ +  V + +   +    R ++ L
Sbjct: 555 IALAYAGTGNNSAVKRLL-HVAVSDSNDDVRRA-AVIALGFVLLRDYTTVP---RIVQLL 609

Query: 483 LQYGEQNIRRAVPLALGLLCISNPKVNVMDTLSRLSHDTDSEVAMAAVISLGLI---GSG 539
            +    ++R     ALG+ C      + +D L  L+ D    V  AA+I+L +I    + 
Sbjct: 610 SKSHNAHVRCGTAFALGIACAGKGLQSAIDVLDPLTKDPVDFVRQAAMIALSMILIQQTE 669

Query: 540 TNNARIAGMLRNLSSYY---YKDANLLFCVRIAQGLVHMGKGLLTLNPYHSDRFLLSPTA 596
             N ++A + +N  S     +++    F   +AQG+++ G   +T+   ++D   L   +
Sbjct: 670 KLNPQVADINKNFLSVITNKHQEGLAKFGACVAQGIMNAGGRNVTIQLENADTGTLDTKS 729

Query: 597 LAGIV 601
           + G+V
Sbjct: 730 VVGLV 734


>pdb|4ADY|A Chain A, Crystal Structure Of 26s Proteasome Subunit Rpn2
 pdb|4ADY|B Chain B, Crystal Structure Of 26s Proteasome Subunit Rpn2
          Length = 963

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 95/424 (22%), Positives = 171/424 (40%), Gaps = 34/424 (8%)

Query: 192 AATFVNAFVNAGFGQDKLMTVPSDASSGGSSGNWLFKNKEHGKMSAAASLGMILLWDVDS 251
           A +  N F +AG          +D S   ++  WL K +   K +A ASLG+I   ++  
Sbjct: 342 AVSVANGFXHAG---------TTDNSFIKANLPWLGKAQNWAKFTATASLGVIHKGNLLE 392

Query: 252 GLAQIDKYF---HSTDNHVIAGALLGVGIVNCGIRNDCDPALALL----SEYVGREDACI 304
           G      Y     ++   +  G+L G+G++  G   D    L  +    S   G ED  +
Sbjct: 393 GKKVXAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDV 452

Query: 305 RI-GAIMGLGISYAGTQNDQIRHKLSTILNDAKSPLDVIAFSAISLGLIYVGSCNEEVAQ 363
            + GA +G+G++  G+ N ++   L  +L +  +     A     L  +  G       +
Sbjct: 453 LLHGASLGIGLAAXGSANIEVYEALKEVLYNDSATSGEAAALGXGLCXLGTGK-----PE 507

Query: 364 AIIFALMDRSESELGEPXXXXXXXXXXXXXXXKQESVEATAEVSKTFNEKIRKYCDMTLL 423
           AI        E++ G                 +QE  +         +E + +Y     +
Sbjct: 508 AIHDXFTYSQETQHGN-ITRGLAVGLALINYGRQELADDLITKXLASDESLLRYGGAFTI 566

Query: 424 SCAYAGTGNVLKVQNLLGHCAQHHEKGEAYQGPAVLGIAMVAMAEELGLEMAIRSLEHLL 483
           + AYAGTGN   V+ LL H A      +  +  AV+ +  V + +        R ++ L 
Sbjct: 567 ALAYAGTGNNSAVKRLL-HVAVSDSNDDVRRA-AVIALGFVLLRD---YTTVPRIVQLLS 621

Query: 484 QYGEQNIRRAVPLALGLLCISNPKVNVMDTLSRLSHDTDSEVAMAAVISLGLI---GSGT 540
           +    ++R     ALG+ C      + +D L  L+ D    V  AA I+L  I    +  
Sbjct: 622 KSHNAHVRCGTAFALGIACAGKGLQSAIDVLDPLTKDPVDFVRQAAXIALSXILIQQTEK 681

Query: 541 NNARIAGMLRNLSSYY---YKDANLLFCVRIAQGLVHMGKGLLTLNPYHSDRFLLSPTAL 597
            N ++A + +N  S     +++    F   +AQG+ + G   +T+   ++D   L   ++
Sbjct: 682 LNPQVADINKNFLSVITNKHQEGLAKFGACVAQGIXNAGGRNVTIQLENADTGTLDTKSV 741

Query: 598 AGIV 601
            G+V
Sbjct: 742 VGLV 745


  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    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,245,686
Number of Sequences: 62578
Number of extensions: 691346
Number of successful extensions: 1479
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1468
Number of HSP's gapped (non-prelim): 10
length of query: 714
length of database: 14,973,337
effective HSP length: 106
effective length of query: 608
effective length of database: 8,340,069
effective search space: 5070761952
effective search space used: 5070761952
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: 55 (25.8 bits)