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= psy15038
         (67 letters)

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

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



>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 1003

 Score = 27.7 bits (60), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 9   EVEIISLLEEQLPQYKLRADTLTEFIGYENQDWFVPCPLQADDPTALTPDQI 60
           + E  +LL E   +Y+  +  + E +  E  DW  P  L  DDP A++ D +
Sbjct: 480 QAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKL--DDPEAVSKDPL 529


>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
          Length = 760

 Score = 27.7 bits (60), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 9   EVEIISLLEEQLPQYKLRADTLTEFIGYENQDWFVPCPLQADDPTALTPDQI 60
           + E  +LL E   +Y+  +  + E +  E  DW  P  L  DDP A++ D +
Sbjct: 237 QAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKL--DDPEAVSKDPL 286


>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
          Length = 977

 Score = 27.7 bits (60), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 9   EVEIISLLEEQLPQYKLRADTLTEFIGYENQDWFVPCPLQADDPTALTPDQI 60
           + E  +LL E   +Y+  +  + E +  E  DW  P  L  DDP A++ D +
Sbjct: 454 QAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKL--DDPEAVSKDPL 503


>pdb|2RH8|A Chain A, Structure Of Apo Anthocyanidin Reductase From Vitis
           Vinifera
 pdb|3HFS|A Chain A, Structure Of Apo Anthocyanidin Reductase From Vitis
           Vinifera
 pdb|3HFS|B Chain B, Structure Of Apo Anthocyanidin Reductase From Vitis
           Vinifera
          Length = 338

 Score = 26.6 bits (57), Expect = 4.0,   Method: Composition-based stats.
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 1   VCCGGDLPEVEIISLLEEQLPQYKLRAD 28
           +CC  +    E+   L ++ PQYK+  D
Sbjct: 264 ICCAANTSVPELAKFLSKRYPQYKVPTD 291


>pdb|3DM5|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins Assembling
           The Ribonucleic Core Of The Signal Recognition Particle
           From The Archaeon Pyrococcus Furiosus.
 pdb|3DM5|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins Assembling
           The Ribonucleic Core Of The Signal Recognition Particle
           From The Archaeon Pyrococcus Furiosus
          Length = 443

 Score = 26.2 bits (56), Expect = 4.4,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 22/29 (75%), Gaps = 1/29 (3%)

Query: 4   GGDLPEVEIISLLEEQLPQYKLRADTLTE 32
           G  LP+ ++IS+ EE+L ++K+  D++TE
Sbjct: 357 GYSLPD-DVISIGEERLKKFKVIMDSMTE 384


>pdb|4GAF|A Chain A, Crystal Structure Of Ebi-005, A Chimera Of Human Il-1beta
           And Il-1ra, Bound To Human Interleukin-1 Receptor Type 1
 pdb|4GAI|A Chain A, Crystal Structure Of Ebi-005, A Chimera Of Human Il-1beta
           And Il-1ra
 pdb|4GAI|B Chain B, Crystal Structure Of Ebi-005, A Chimera Of Human Il-1beta
           And Il-1ra
          Length = 153

 Score = 25.4 bits (54), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 16  LEEQLPQYKLRADTLTEFIGYENQDWFVPCPLQADDPTALT--PDQ 59
           +E++    K+  +   EF   +  +WF+   ++AD P +LT  PD+
Sbjct: 94  MEKRFVFNKIEINNKLEFESAQFPNWFLCTAMEADQPVSLTNMPDE 139


  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
   0.320    0.142    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,223,557
Number of Sequences: 62578
Number of extensions: 73721
Number of successful extensions: 123
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 120
Number of HSP's gapped (non-prelim): 7
length of query: 67
length of database: 14,973,337
effective HSP length: 38
effective length of query: 29
effective length of database: 12,595,373
effective search space: 365265817
effective search space used: 365265817
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)