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= 026728
         (234 letters)

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

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



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

 Score =  130 bits (327), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 58/114 (50%), Positives = 75/114 (65%), Gaps = 1/114 (0%)

Query: 11  AMQEILLEFRAGKMTFDGKKVVPDSRKGLVRIARGEHGLIHFQWLDRTRNVVEDDQIVFP 70
           A  + L+EFRAGKM+  G  V PD RKGLV I + +  LIHF W DRT   VEDD I+FP
Sbjct: 22  ASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGNVEDDLIIFP 81

Query: 71  HEAVFEKVNQA-SGRVYILKFNTDDRKFFLWMQEPKAEEDSQLCNSVNYFINRP 123
            +  F++V Q  SGRVY+LKF    ++ F WMQEPK ++D + C  VN ++N P
Sbjct: 82  DDCEFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNEYLNNP 135



 Score = 28.1 bits (61), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 9/72 (12%)

Query: 163 GEAISDVTSSSGPVKLEDLQRIFSNI----GPADITEXXXXXXXXXXXXXXXXXMPLIET 218
           G   S   S + P++L DLQ I + +    GPA   +                  P++  
Sbjct: 253 GNGASTAASPTQPIQLSDLQSILATMNVPAGPAGGQQVDLASVLTPEIMA-----PILAN 307

Query: 219 LPLEQRLAPYLP 230
             +++RL PYLP
Sbjct: 308 ADVQERLLPYLP 319


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

 Score =  126 bits (316), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 57/111 (51%), Positives = 73/111 (65%), Gaps = 1/111 (0%)

Query: 14  EILLEFRAGKMTFDGKKVVPDSRKGLVRIARGEHGLIHFQWLDRTRNVVEDDQIVFPHEA 73
           + L+EFRAGKM+  G  V PD RKGLV I + +  LIHF W DRT   VEDD I+FP + 
Sbjct: 24  KYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGTVEDDLIIFPDDC 83

Query: 74  VFEKVNQA-SGRVYILKFNTDDRKFFLWMQEPKAEEDSQLCNSVNYFINRP 123
            F++V Q  SGRVY+LKF    ++ F WMQEPK ++D + C  VN  +N P
Sbjct: 84  EFKRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNECLNNP 134


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

 Score =  121 bits (304), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 56/107 (52%), Positives = 71/107 (66%), Gaps = 1/107 (0%)

Query: 16  LLEFRAGKMTFDGKKVVPDSRKGLVRIARGEHGLIHFQWLDRTRNVVEDDQIVFPHEAVF 75
           L+EFRAGKM+  G  V PD RKGLV I + +  LIHF W DRT   VEDD I+FP +  F
Sbjct: 2   LVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGTVEDDLIIFPDDCEF 61

Query: 76  EKVNQA-SGRVYILKFNTDDRKFFLWMQEPKAEEDSQLCNSVNYFIN 121
           ++V Q  SGRVY+LKF    ++ F WMQEPK ++D + C  VN  +N
Sbjct: 62  KRVPQCPSGRVYVLKFKAGSKRLFFWMQEPKTDQDEEHCRKVNECLN 108


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

 Score = 40.0 bits (92), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 51/103 (49%), Gaps = 11/103 (10%)

Query: 11  AMQEILLEFRAGKMTF--DGKKVVPDSRKGLVRIARGEH---GLIHFQWLDRTRNVVED- 64
           +M   +++FRAG   +  D +   P   +G + I   E    G   F+W    + V  + 
Sbjct: 2   SMSSTVIKFRAGVCEYNEDSRLCTPIPVQGEIEIKPNEEEELGFWDFEWRPTEKPVGREL 61

Query: 65  ---DQIVFPHEAVFEKVNQA-SGRVYILKFNTDDRKFFLWMQE 103
                I+ P E ++  +  + SGR++ L F++++R +F W+QE
Sbjct: 62  DPISLILIPGETMWVPIKSSKSGRIFALVFSSNER-YFFWLQE 103


>pdb|4HVT|A Chain A, Structure Of A Post-Proline Cleaving Enzyme From
           Rickettsia Typhi
          Length = 711

 Score = 31.6 bits (70), Expect = 0.41,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 10/69 (14%)

Query: 65  DQIVFP-HEAVFEKVNQASGRVYILKFNTDDRKFFLWMQEPKAEEDSQLCNSVNYFINRP 123
           DQ V P H  +FE         Y+L  N + + +FL  ++      S L  S NYFIN  
Sbjct: 649 DQRVHPWHGRIFE---------YVLAQNPNTKTYFLESKDSGHGSGSDLKESANYFINLY 699

Query: 124 LVFVNEEEL 132
             F N  +L
Sbjct: 700 TFFANALKL 708


  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
   0.317    0.135    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,215,520
Number of Sequences: 62578
Number of extensions: 238181
Number of successful extensions: 490
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 481
Number of HSP's gapped (non-prelim): 8
length of query: 234
length of database: 14,973,337
effective HSP length: 96
effective length of query: 138
effective length of database: 8,965,849
effective search space: 1237287162
effective search space used: 1237287162
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)