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= 019478
         (340 letters)

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

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



>pdb|1FS2|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FS2|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
          Length = 272

 Score = 32.7 bits (73), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 56/128 (43%), Gaps = 20/128 (15%)

Query: 18  VDWISRLPDEILVNIISRLAVREAARTSVLSSRWKYLWTFTTCLNFSALKMLWNVKKDPA 77
           V W S LPDE+L+ I S L + E  + S +  RW  L         ++ + LW       
Sbjct: 7   VSWDS-LPDELLLGIFSCLCLPELLKVSGVCKRWYRL---------ASDESLWQ------ 50

Query: 78  TLEEERYNYINWVNDVLDSHMGLCINEFRLCFELRN--SHGSFITHWIFTALAKKVQKLE 135
           TL+E R  +++  N V++      I     C +L+N    G  ++  I   LAK    + 
Sbjct: 51  TLDEFRVQHMDLSNSVIEVSTLHGI--LSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVR 108

Query: 136 LNLHPVGG 143
           LNL    G
Sbjct: 109 LNLSGCSG 116


>pdb|3A3T|A Chain A, The Oxidoreductase Nmdsba1 From N. Meningitidis
 pdb|3A3T|B Chain B, The Oxidoreductase Nmdsba1 From N. Meningitidis
 pdb|3A3T|C Chain C, The Oxidoreductase Nmdsba1 From N. Meningitidis
 pdb|3A3T|D Chain D, The Oxidoreductase Nmdsba1 From N. Meningitidis
 pdb|3A3T|E Chain E, The Oxidoreductase Nmdsba1 From N. Meningitidis
 pdb|3A3T|F Chain F, The Oxidoreductase Nmdsba1 From N. Meningitidis
          Length = 210

 Score = 28.9 bits (63), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 15/28 (53%)

Query: 187 EVLEFFIYSCPLLARLRVVFSLDLLSLK 214
           EVLEFF Y CP  A L  V S    S K
Sbjct: 44  EVLEFFGYFCPHCAHLEPVLSKHAKSFK 71


>pdb|3DVW|A Chain A, Crystal Structure Of Reduced Dsba1 From Neisseria
           Meningitidis
          Length = 193

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 15/28 (53%)

Query: 187 EVLEFFIYSCPLLARLRVVFSLDLLSLK 214
           EVLEFF Y CP  A L  V S    S K
Sbjct: 27  EVLEFFGYFCPHCAHLEPVLSKHAKSFK 54


>pdb|3HZ8|A Chain A, Crystal Structure Of The Oxidized T176v Dsba1 Mutant
          Length = 193

 Score = 28.9 bits (63), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 15/28 (53%)

Query: 187 EVLEFFIYSCPLLARLRVVFSLDLLSLK 214
           EVLEFF Y CP  A L  V S    S K
Sbjct: 27  EVLEFFGYFCPHCAHLEPVLSKHAKSFK 54


  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
   0.325    0.139    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,258,258
Number of Sequences: 62578
Number of extensions: 349867
Number of successful extensions: 842
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 838
Number of HSP's gapped (non-prelim): 8
length of query: 340
length of database: 14,973,337
effective HSP length: 99
effective length of query: 241
effective length of database: 8,778,115
effective search space: 2115525715
effective search space used: 2115525715
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)