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= psy11405
         (76 letters)

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

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



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

 Score = 94.0 bits (232), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 44/69 (63%), Positives = 54/69 (78%), Gaps = 3/69 (4%)

Query: 1  MPSGGALFGSTVSRSQ---SKNLVEFKAGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFC 57
          M + GALF S V  S+   +K LVEF+AGKM++KG  V PDKRKGLVY+ Q+DDSL+HFC
Sbjct: 5  MTTSGALFPSLVPGSRGASNKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFC 64

Query: 58 WKDRQSGSV 66
          WKDR SG+V
Sbjct: 65 WKDRTSGNV 73


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

 Score = 90.1 bits (222), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 43/67 (64%), Positives = 53/67 (79%), Gaps = 3/67 (4%)

Query: 3  SGGALFGSTVSRSQ---SKNLVEFKAGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWK 59
          + GALF S V  S+   +K LVEF+AGKM++KG  V PDKRKGLVY+ Q+DDSL+HFCWK
Sbjct: 6  TSGALFPSLVPGSRGSSTKYLVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWK 65

Query: 60 DRQSGSV 66
          DR SG+V
Sbjct: 66 DRTSGTV 72


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

 Score = 82.0 bits (201), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 35/47 (74%), Positives = 42/47 (89%)

Query: 20 LVEFKAGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSV 66
          LVEF+AGKM++KG  V PDKRKGLVY+ Q+DDSL+HFCWKDR SG+V
Sbjct: 2  LVEFRAGKMSLKGTTVTPDKRKGLVYIQQTDDSLIHFCWKDRTSGTV 48


>pdb|1AD0|B Chain B, Fab Fragment Of Engineered Human Monoclonal Antibody A5b7
 pdb|1AD0|D Chain D, Fab Fragment Of Engineered Human Monoclonal Antibody A5b7
          Length = 220

 Score = 27.3 bits (59), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 5/38 (13%)

Query: 29  TMKGKM-VHPDKRKGLVYVH----QSDDSLMHFCWKDR 61
           ++KG+  +  DK K  +Y+     Q++DS +++C +DR
Sbjct: 65  SVKGRFTISRDKSKSTLYLQMNTLQAEDSAIYYCTRDR 102


>pdb|2KXI|A Chain A, Solution Nmr Structure Of The Apoform Of Nare (Nmb1343)
          Length = 153

 Score = 26.6 bits (57), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 14/33 (42%)

Query: 26 GKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCW 58
          GK    GK  H    K  VY HQ +  L   C+
Sbjct: 36 GKFKYDGKATHGPSVKNAVYAHQIETGLYDGCY 68


>pdb|3FOC|A Chain A, Tryptophanyl-Trna Synthetase From Giardia Lamblia
 pdb|3FOC|B Chain B, Tryptophanyl-Trna Synthetase From Giardia Lamblia
          Length = 451

 Score = 25.8 bits (55), Expect = 6.5,   Method: Composition-based stats.
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 29 TMKGKMVHPDKRKGLVYVHQSDDSLMHF 56
          T+ G   HP  R+GL Y H+  +  + +
Sbjct: 58 TVTGTKAHPMLRRGLFYAHRDFEEFLSY 85


  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    0.130    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,239,434
Number of Sequences: 62578
Number of extensions: 72299
Number of successful extensions: 246
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 12
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
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: 45 (21.9 bits)