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= 039662
         (366 letters)

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

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



>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 = 28.5 bits (62), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 6  LSDDMMIETLSRLPVKSLMRFQCVCKSWYDLVKDPNF 42
          L D++++   S L +  L++   VCK WY L  D + 
Sbjct: 12 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESL 48


>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 = 28.5 bits (62), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 6  LSDDMMIETLSRLPVKSLMRFQCVCKSWYDLVKDPNF 42
          L D++++   S L +  L++   VCK WY L  D + 
Sbjct: 12 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESL 48


>pdb|1FS1|A Chain A, Insights Into Scf Ubiquitin Ligases From The Structure
          Of The Skp1-Skp2 Complex
 pdb|1FS1|C Chain C, Insights Into Scf Ubiquitin Ligases From The Structure
          Of The Skp1-Skp2 Complex
          Length = 53

 Score = 28.1 bits (61), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 6  LSDDMMIETLSRLPVKSLMRFQCVCKSWYDLVKDPNF 42
          L D++++   S L +  L++   VCK WY L  D + 
Sbjct: 12 LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESL 48


>pdb|1LDK|E Chain E, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
          Ligase Complex
          Length = 41

 Score = 28.1 bits (61), Expect = 8.8,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 6  LSDDMMIETLSRLPVKSLMRFQCVCKSWYDLVKD 39
          L D++++   S L +  L++   VCK WY L  D
Sbjct: 4  LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASD 37


  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    0.140    0.455 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,122,781
Number of Sequences: 62578
Number of extensions: 542142
Number of successful extensions: 1229
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1223
Number of HSP's gapped (non-prelim): 7
length of query: 366
length of database: 14,973,337
effective HSP length: 100
effective length of query: 266
effective length of database: 8,715,537
effective search space: 2318332842
effective search space used: 2318332842
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)