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= psy11404
         (251 letters)

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

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



>pdb|2KR0|A Chain A, A Proteasome Protein
          Length = 411

 Score =  192 bits (487), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 91/153 (59%), Positives = 110/153 (71%), Gaps = 21/153 (13%)

Query: 1   MTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEDLIIFPDDCEFKKVPQCTT 60
           M++KG  V PDKRKGLVY+ Q+DDSL+HFCWKDR SG+V +DLIIFPDDCEFK+VPQC +
Sbjct: 35  MSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFPDDCEFKRVPQCPS 94

Query: 61  GRVYVLKFKSSNRKLFFWLQEPKTDKDDENARKVNEVLNNPPTPGS-QRSDSSGRVEGDI 119
           GRVYVLKFK+ +++LFFW+QEPKTD+D+E+ RKVNE LNNPP PG+   S SSG      
Sbjct: 95  GRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNPPMPGALGASGSSGH----- 149

Query: 120 XXXXXXXXXXXXXXFFGGQINQMGGLSSLLGTM 152
                           GG+    GGL SLLG M
Sbjct: 150 -----------ELSALGGE----GGLQSLLGNM 167



 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 35/46 (76%)

Query: 165 EAVSMFSAALQSGQLGPVVQQFDVSNEAVAATTQGNMEEFVRALQN 210
           +A+ MFSAAL SGQLGP++ QF +  EAV A  +G++E F +A+QN
Sbjct: 342 QALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQN 387


>pdb|2R2Y|A Chain A, Crystal Structure Of The Proteasomal Rpn13 Pru-Domain
          Length = 153

 Score =  180 bits (457), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 76/104 (73%), Positives = 93/104 (89%)

Query: 1   MTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEDLIIFPDDCEFKKVPQCTT 60
           M++KG  V PDKRKGLVY+ Q+DDSL+HFCWKDR SG+V +DLIIFPDDCEFK+VPQC +
Sbjct: 34  MSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGTVEDDLIIFPDDCEFKRVPQCPS 93

Query: 61  GRVYVLKFKSSNRKLFFWLQEPKTDKDDENARKVNEVLNNPPTP 104
           GRVYVLKFK+ +++LFFW+QEPKTD+D+E+ RKVNE LNNPP P
Sbjct: 94  GRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNECLNNPPMP 137


>pdb|2Z59|A Chain A, Complex Structures Of Mouse Rpn13 (22-130aa) And Ubiquitin
          Length = 109

 Score =  171 bits (433), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 73/100 (73%), Positives = 90/100 (90%)

Query: 1   MTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEDLIIFPDDCEFKKVPQCTT 60
           M++KG  V PDKRKGLVY+ Q+DDSL+HFCWKDR SG+V +DLIIFPDDCEFK+VPQC +
Sbjct: 10  MSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGTVEDDLIIFPDDCEFKRVPQCPS 69

Query: 61  GRVYVLKFKSSNRKLFFWLQEPKTDKDDENARKVNEVLNN 100
           GRVYVLKFK+ +++LFFW+QEPKTD+D+E+ RKVNE LNN
Sbjct: 70  GRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNECLNN 109


>pdb|2KQZ|A Chain A, Fragment Of Proteasome Protein
          Length = 155

 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 35/46 (76%)

Query: 165 EAVSMFSAALQSGQLGPVVQQFDVSNEAVAATTQGNMEEFVRALQN 210
           +A+ MFSAAL SGQLGP++ QF +  EAV A  +G++E F +A+QN
Sbjct: 86  QALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQN 131


>pdb|2L5V|A Chain A, Solution Structure Of The C-Terminal Domain Of Hrpn13
          Length = 150

 Score = 54.7 bits (130), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 35/46 (76%)

Query: 165 EAVSMFSAALQSGQLGPVVQQFDVSNEAVAATTQGNMEEFVRALQN 210
           +A+ MFSAAL SGQLGP++ QF +  EAV A  +G++E F +A+QN
Sbjct: 81  QALGMFSAALASGQLGPLMCQFGLPAEAVEAANKGDVEAFAKAMQN 126


>pdb|4B4T|X Chain X, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 156

 Score = 36.6 bits (83), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 43  LIIFPDDCEFKKVPQCTTGRVYVLKFKSSNRKLFFWLQE 81
           LI+ P +  +  +    +GR++ L F SSN + FFWLQE
Sbjct: 66  LILIPGETMWVPIKSSKSGRIFALVF-SSNERYFFWLQE 103


>pdb|2Z4D|A Chain A, Nmr Structures Of Yeast Proteasome Component Rpn13
          Length = 96

 Score = 31.2 bits (69), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)

Query: 43 LIIFPDDCEFKKVPQCTTGRVYVLKFKSSNRKLFFWL 79
          LI+ P +  +  +    +GR++ L F SSN + FFWL
Sbjct: 61 LILIPGETMWVPIKSSKSGRIFALVF-SSNERYFFWL 96


  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
   0.314    0.129    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,425,603
Number of Sequences: 62578
Number of extensions: 225505
Number of successful extensions: 417
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 411
Number of HSP's gapped (non-prelim): 8
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)