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= psy14394
         (200 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 = 27.3 bits (59), Expect = 5.4,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 6/63 (9%)

Query: 3   GLVSRSPFSEQG------VIIGIVNSFVHVVMYSYYFLAALGPHMQKHLWWKKYITRLQL 56
           GL+++S  S  G        + + N F+H       F+ A  P + K   W K+     L
Sbjct: 312 GLLNKSKSSLDGKFSLFHTAVSVANGFMHAGTTDNSFIKANLPWLGKAQNWAKFTATASL 371

Query: 57  GVI 59
           GVI
Sbjct: 372 GVI 374


>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 = 26.6 bits (57), Expect = 8.6,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 3   GLVSRSPFSEQG------VIIGIVNSFVHVVMYSYYFLAALGPHMQKHLWWKKYITRLQL 56
           GL+++S  S  G        + + N F H       F+ A  P + K   W K+     L
Sbjct: 323 GLLNKSKSSLDGKFSLFHTAVSVANGFXHAGTTDNSFIKANLPWLGKAQNWAKFTATASL 382

Query: 57  GVI 59
           GVI
Sbjct: 383 GVI 385


  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
   0.327    0.138    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,442,933
Number of Sequences: 62578
Number of extensions: 193451
Number of successful extensions: 395
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 7
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)