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= psy6263
         (913 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 = 50.4 bits (119), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 61/258 (23%), Positives = 103/258 (39%), Gaps = 25/258 (9%)

Query: 354 ASTFVNAFVNAGFSRDKLVSVEDGNKWMYKNKQHGMLSAAASLGLIYLWDVDGGLTPIDK 413
           A +  N F++AG + +  +       W+ K +     +A ASLG+I+  ++  G   +  
Sbjct: 331 AVSVANGFMHAGTTDNSFIKAN--LPWLGKAQNWAKFTATASLGVIHKGNLLEGKKVMAP 388

Query: 414 YL---YTSEDYIKAGALLALGIVNCGV-RNECDPALALLSDYVLNDSIT--------LRI 461
           YL     S  +IK G+L  LG++  G  R+  D     L + ++ +S T        L  
Sbjct: 389 YLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTD----YLKNIIVENSGTSGDEDVDVLLH 444

Query: 462 XXXXXXXXXXXXTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAIL 521
                       +   EV   L  VL +  +T      AA+   L  +GTG  E    + 
Sbjct: 445 GASLGIGLAAMGSANIEVYEALKEVLYNDSATSGEA--AALGMGLCMLGTGKPEAIHDMF 502

Query: 522 QTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSMAKMMLKMC 581
                    E Q G+ +R L + LA+   G+++  D  +  +    +             
Sbjct: 503 TY-----SQETQHGNITRGLAVGLALINYGRQELADDLITKMLASDESLLRYGGAFTIAL 557

Query: 582 AYAGSGDVLVVQEFLHVC 599
           AYAG+G+   V+  LHV 
Sbjct: 558 AYAGTGNNSAVKRLLHVA 575


>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 = 37.4 bits (85), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 58/260 (22%), Positives = 98/260 (37%), Gaps = 29/260 (11%)

Query: 354 ASTFVNAFVNAGFSRDKLVSVEDGNKWMYKNKQHGMLSAAASLGLIYLWDVDGGLTPIDK 413
           A +  N F +AG + +  +       W+ K +     +A ASLG+I+  ++  G      
Sbjct: 342 AVSVANGFXHAGTTDNSFIKAN--LPWLGKAQNWAKFTATASLGVIHKGNLLEGKKVXAP 399

Query: 414 YL---YTSEDYIKAGALLALGIVNCGV-RNECDPALALLSDYVLNDSIT--------LRI 461
           YL     S  +IK G+L  LG++  G  R+  D     L + ++ +S T        L  
Sbjct: 400 YLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTD----YLKNIIVENSGTSGDEDVDVLLH 455

Query: 462 XXXXXXXXXXXXTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGT--GYHEVASA 519
                       +   EV   L  VL +  +T    A        +  G     H+  + 
Sbjct: 456 GASLGIGLAAXGSANIEVYEALKEVLYNDSATSGEAAALGXGLCXLGTGKPEAIHDXFTY 515

Query: 520 ILQTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSMAKMMLK 579
             +T         Q G+ +R L + LA+   G+++  D  +       +           
Sbjct: 516 SQET---------QHGNITRGLAVGLALINYGRQELADDLITKXLASDESLLRYGGAFTI 566

Query: 580 MCAYAGSGDVLVVQEFLHVC 599
             AYAG+G+   V+  LHV 
Sbjct: 567 ALAYAGTGNNSAVKRLLHVA 586


>pdb|1FIW|A Chain A, Three-Dimensional Structure Of Beta-Acrosin From Ram
           Spermatozoa
          Length = 290

 Score = 30.0 bits (66), Expect = 5.6,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 124 YCLMAKQKDVGDWGHEYVRQLEAEIAEEWATNKYEKPQLLELIEDIIQFDMKHNAEIQAC 183
           +C   K+K V DW     R +      EW TNK  KP L E   + I    K++A  +A 
Sbjct: 47  HCFRIKKK-VTDW-----RLIFGAKEVEWGTNKPVKPPLQERYVEKIIIHEKYSASSEAN 100

Query: 184 DL-LMEI 189
           D+ LM+I
Sbjct: 101 DIALMKI 107


>pdb|1GJU|A Chain A, Maltosyltransferase From Thermotoga Maritima
 pdb|1GJW|A Chain A, Thermotoga Maritima Maltosyltransferase Complex With
           Maltose
          Length = 637

 Score = 29.3 bits (64), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 11/43 (25%), Positives = 26/43 (60%)

Query: 284 ELPDEMPDKNDLQIIMTNSHINDHFHSLARELDIMEPKTPEEV 326
           ELP ++PD+++L+II    ++  H        ++++P+  E++
Sbjct: 239 ELPFKVPDEDELEIIYNKENVKRHLKKFTLPPNLIDPQKWEKI 281


  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    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,481,404
Number of Sequences: 62578
Number of extensions: 987889
Number of successful extensions: 2311
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2304
Number of HSP's gapped (non-prelim): 10
length of query: 913
length of database: 14,973,337
effective HSP length: 108
effective length of query: 805
effective length of database: 8,214,913
effective search space: 6613004965
effective search space used: 6613004965
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: 56 (26.2 bits)