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= psy3867
         (521 letters)

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

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



>pdb|2OOI|A Chain A, The Crystal Structure Of Gene Product Sa0254 From
           Staphylocococcus Aureus Subsp. Aureus N315
 pdb|2OOI|B Chain B, The Crystal Structure Of Gene Product Sa0254 From
           Staphylocococcus Aureus Subsp. Aureus N315
          Length = 162

 Score = 32.7 bits (73), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 2/92 (2%)

Query: 20  SSLIVVNVMDPHPRACSKEQVLNGDEEITQNIRVVFSFSRADKLCPRCNTNNGEVVLRLK 79
           S ++V   M   P++   E  LN D+ +    R+   F   D LC   +  + E+V  L 
Sbjct: 22  SKVLVFKEMATPPKSVQDELQLNADDTVYYLERL--RFVDDDVLCIEYSYYHKEIVKYLN 79

Query: 80  DIYCKACLLQYLNHKFRAALGKSKMMRPQDKV 111
           D   K  +  YL    +  +G S +    DK+
Sbjct: 80  DDIAKGSIFDYLESNMKLRIGFSDIFFNVDKL 111


>pdb|1IOK|A Chain A, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
 pdb|1IOK|B Chain B, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
 pdb|1IOK|C Chain C, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
 pdb|1IOK|D Chain D, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
 pdb|1IOK|E Chain E, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
 pdb|1IOK|F Chain F, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
 pdb|1IOK|G Chain G, Crystal Structure Of Chaperonin-60 From Paracoccus
           Denitrificans
          Length = 545

 Score = 28.5 bits (62), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 28/66 (42%), Gaps = 9/66 (13%)

Query: 439 SVNGSEDIPNQIVNGMQYTPNEKVSRTEDNEG-------PDNLQRSLCYACQYVVKDMTS 491
           S NG   I  QI   MQ   NE V   E+N+G        + +Q    Y   Y V +  +
Sbjct: 151 SANGESFIGQQIAEAMQRVGNEGVITVEENKGMETEVEVVEGMQFDRGYLSPYFVTN--A 208

Query: 492 DKDIGE 497
           DK I E
Sbjct: 209 DKMIAE 214


  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    0.130    0.367 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,384,797
Number of Sequences: 62578
Number of extensions: 505100
Number of successful extensions: 1247
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1245
Number of HSP's gapped (non-prelim): 6
length of query: 521
length of database: 14,973,337
effective HSP length: 103
effective length of query: 418
effective length of database: 8,527,803
effective search space: 3564621654
effective search space used: 3564621654
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)