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= psy2304
         (85 letters)

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

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



>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader
           (Replication Factor C, Rfc) Bound To The Dna Sliding
           Clamp (Proliferating Cell Nuclear Antigen, Pcna)
          Length = 354

 Score = 52.0 bits (123), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 35/53 (66%)

Query: 8   TPSKKKIDIMTTASNYHIEVNPNDAGIYDRVVVMELIKNVAQTNQLDPNGQRD 60
           T S +K+++   +S YH+E+ P+D G  DR+V+ EL+K VAQ  Q+D    +D
Sbjct: 77  TASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKD 129


>pdb|1LNS|A Chain A, Crystal Structure Analysis Of The X-Prolyl Dipeptidyl
           Aminopeptidase From Lactococcus Lactis
          Length = 763

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 2/35 (5%)

Query: 10  SKKKIDIMTTASNYHIEVN--PNDAGIYDRVVVME 42
           S +K+ ++ TAS YH+ +N   ND  ++D  V +E
Sbjct: 197 STEKLPVVMTASPYHLGINDKANDLALHDMNVELE 231


  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    0.132    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,552,732
Number of Sequences: 62578
Number of extensions: 88500
Number of successful extensions: 120
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 119
Number of HSP's gapped (non-prelim): 2
length of query: 85
length of database: 14,973,337
effective HSP length: 53
effective length of query: 32
effective length of database: 11,656,703
effective search space: 373014496
effective search space used: 373014496
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)