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= 028616
         (206 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 = 28.1 bits (61), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 35/152 (23%), Positives = 56/152 (36%), Gaps = 23/152 (15%)

Query: 1   MSDSIVAQIAGRLSAVTFLDLSYCSKIGAPALEAIGKHCKLL--------------VVLC 46
           +SD IV  +A   S +  L+LS CS     AL+ +   C  L               V  
Sbjct: 92  LSDPIVNTLAKN-SNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQV 150

Query: 47  RNMHPLDTADKLS--------QDDEANAIASTMPKLKRLEMAYHVISTEIVLKILSSCAL 98
              H  +T  +L+        Q  + + +    P L  L+++  V+      +       
Sbjct: 151 AVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNY 210

Query: 99  LEFLDLRGCWDVKLDDKFMKGNFPNLKVLGPF 130
           L+ L L  C+D+  +     G  P LK L  F
Sbjct: 211 LQHLSLSRCYDIIPETLLELGEIPTLKTLQVF 242


>pdb|1FQV|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|E Chain E, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|G Chain G, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|I Chain I, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|K Chain K, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|M Chain M, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|1FQV|O Chain O, Insights Into Scf Ubiquitin Ligases From The Structure Of
           The Skp1-Skp2 Complex
 pdb|2ASS|B Chain B, Crystal Structure Of The Skp1-Skp2-Cks1 Complex
 pdb|2AST|B Chain B, Crystal Structure Of Skp1-Skp2-Cks1 In Complex With A P27
           Peptide
          Length = 336

 Score = 28.1 bits (61), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 35/152 (23%), Positives = 56/152 (36%), Gaps = 23/152 (15%)

Query: 1   MSDSIVAQIAGRLSAVTFLDLSYCSKIGAPALEAIGKHCKLL--------------VVLC 46
           +SD IV  +A   S +  L+LS CS     AL+ +   C  L               V  
Sbjct: 130 LSDPIVNTLAKN-SNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQV 188

Query: 47  RNMHPLDTADKLS--------QDDEANAIASTMPKLKRLEMAYHVISTEIVLKILSSCAL 98
              H  +T  +L+        Q  + + +    P L  L+++  V+      +       
Sbjct: 189 AVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNY 248

Query: 99  LEFLDLRGCWDVKLDDKFMKGNFPNLKVLGPF 130
           L+ L L  C+D+  +     G  P LK L  F
Sbjct: 249 LQHLSLSRCYDIIPETLLELGEIPTLKTLQVF 280


  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
   0.321    0.139    0.440 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,518,324
Number of Sequences: 62578
Number of extensions: 198331
Number of successful extensions: 342
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 340
Number of HSP's gapped (non-prelim): 4
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)