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= psy11733
         (971 letters)

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

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



>pdb|4B4T|R Chain R, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 429

 Score = 81.3 bits (199), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/270 (24%), Positives = 120/270 (44%), Gaps = 9/270 (3%)

Query: 186 DLGDHYLDCGDLSNALKCYSRARDYCTNGKHVVDMCLNVIRVSVYLQNWSHVLSYVNKAE 245
           +LG++Y   GD  NA K   ++     +    +D+ L + R+  +  +  +V     K E
Sbjct: 136 NLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYV---KEKLE 192

Query: 246 ATPDFAEGKDNNQAVFTKLKVAAGLAELATRKYKTAARFFLQAHFDYCDFPELLSPNNIA 305
           A     E K  +     + K   G+  LA R +K AA+  + +   +    EL S  +IA
Sbjct: 193 AVNSMIE-KGGDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDSLATFTSI-ELTSYESIA 250

Query: 306 TYGGLCALATFDRSELEKQVIFSSGFKLFLELEPQLRDI---LVQFYNSKYATCLNLLAQ 362
           TY  +  L T +R++L+ +VI S      +     L+ I    +  Y S YA+    L +
Sbjct: 251 TYASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLE 310

Query: 363 IMDNLLLD-MYIAPHVNTLYTQIRNRALIQYFSPYLSADLNKMSVAFNTTIQALENELMT 421
              N+L+   Y+  H +    ++R +   Q    Y +  L  M+ AF  ++  L+N+L  
Sbjct: 311 TYANVLIPCKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGK 370

Query: 422 LILDGQIQARIDSHNKILYAKQQDQRSTTF 451
            I + Q+   ID  N I+   + D ++  +
Sbjct: 371 FIPNKQLNCVIDRVNGIVETNRPDNKNAQY 400


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

 Score = 36.2 bits (82), Expect = 0.091,   Method: Compositional matrix adjust.
 Identities = 24/116 (20%), Positives = 50/116 (43%)

Query: 360 LAQIMDNLLLDMYIAPHVNTLYTQIRNRALIQYFSPYLSADLNKMSVAFNTTIQALENEL 419
           L Q    L+ D     H N LY  +    L +   P+   +++ +S       Q +E +L
Sbjct: 318 LKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLDTQQVEGKL 377

Query: 420 MTLILDGQIQARIDSHNKILYAKQQDQRSTTFEKSLNVGKEYARKSNMLILRSAMI 475
             +ILD      +D  N  LY  +   +  T++ +L +  +  +  + L  +++++
Sbjct: 378 SQMILDKIFYGVLDQGNGWLYVYETPNQDATYDSALELVGQLNKVVDQLFEKASVL 433


>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 = 33.9 bits (76), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 18/87 (20%), Positives = 39/87 (44%)

Query: 370 DMYIAPHVNTLYTQIRNRALIQYFSPYLSADLNKMSVAFNTTIQALENELMTLILDGQIQ 429
           D+ +  H+ TLY  +  + L +   PY    +  ++ +    +  +E +L  +ILD +  
Sbjct: 288 DVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFS 347

Query: 430 ARIDSHNKILYAKQQDQRSTTFEKSLN 456
             +D    +L   ++     T+E+ L 
Sbjct: 348 GILDQGEGVLIVFEETPVDKTYERVLE 374


  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    0.135    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,025,920
Number of Sequences: 62578
Number of extensions: 1028032
Number of successful extensions: 2173
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2158
Number of HSP's gapped (non-prelim): 24
length of query: 971
length of database: 14,973,337
effective HSP length: 108
effective length of query: 863
effective length of database: 8,214,913
effective search space: 7089469919
effective search space used: 7089469919
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)