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= psy9993
         (605 letters)

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

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



>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
           Novel E3 Ligase
          Length = 622

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/201 (26%), Positives = 80/201 (39%), Gaps = 25/201 (12%)

Query: 13  GLTKLGLTDRGLTNLGLTDRGLTNLGLTDRGLTNLGLTDRGLTNLGLTDRGLTNLGLTDR 72
           GL +L +    LT+L     GL  L +    LT+L +   GL  L ++D  L +L     
Sbjct: 102 GLLELSIFSNPLTHLPALPSGLCKLWIFGNQLTSLPVLPPGLQELSVSDNQLASLPALPS 161

Query: 73  VLTNLGLTDRGLTNLGLTDRGLTNLGLTDRDVTDDGVGAALGYSASEIDSELNYSWNYEP 132
            L  L   +  LT+L +   GL  L ++D  +           S   + SEL   W Y  
Sbjct: 162 ELCKLWAYNNQLTSLPMLPSGLQELSVSDNQLA----------SLPTLPSELYKLWAY-- 209

Query: 133 NGMAHYSRSDLLTDRGLTKLGLTDRGLTNLGLTDRGLTNLGLTDRGLTNLGLTDRGLTNL 192
                        +  LT L     GL  L ++   LT+L +    L  L ++   LT+L
Sbjct: 210 -------------NNRLTSLPALPSGLKELIVSGNRLTSLPVLPSELKELMVSGNRLTSL 256

Query: 193 GLTDRGLTNLGLTDRGLTNLG 213
            +   GL +L +    LT L 
Sbjct: 257 PMLPSGLLSLSVYRNQLTRLP 277


>pdb|2J5W|A Chain A, Ceruloplasmin Revisited: Structural And Functional Roles
           Of Various Metal Cation Binding Sites
          Length = 1065

 Score = 29.3 bits (64), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 11/59 (18%)

Query: 128 WNYEPNGMAHYSRSDLLTDRGLTKLG-----LTDRGLTNLGLTDRGLTNLGLTDRGLTN 181
           WNY P+G+      D+ T   LT  G       ++G T +G + + L     TD   TN
Sbjct: 383 WNYAPSGI------DIFTKENLTAPGSDSAVFFEQGTTRIGGSYKKLVYREYTDASFTN 435


>pdb|1KCW|A Chain A, X-Ray Crystal Structure Of Human Ceruloplasmin At 3.0
           Angstroms
          Length = 1046

 Score = 29.3 bits (64), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 11/59 (18%)

Query: 128 WNYEPNGMAHYSRSDLLTDRGLTKLG-----LTDRGLTNLGLTDRGLTNLGLTDRGLTN 181
           WNY P+G+      D+ T   LT  G       ++G T +G + + L     TD   TN
Sbjct: 364 WNYAPSGI------DIFTKENLTAPGSDSAVFFEQGTTRIGGSYKKLVYREYTDASFTN 416


  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
   0.316    0.141    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,483,433
Number of Sequences: 62578
Number of extensions: 738289
Number of successful extensions: 1700
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1555
Number of HSP's gapped (non-prelim): 79
length of query: 605
length of database: 14,973,337
effective HSP length: 104
effective length of query: 501
effective length of database: 8,465,225
effective search space: 4241077725
effective search space used: 4241077725
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: 54 (25.4 bits)