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= 019659
         (337 letters)

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

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



>pdb|2OVP|B Chain B, Structure Of The Skp1-Fbw7 Complex
 pdb|2OVQ|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegc Complex
 pdb|2OVR|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegn Complex
          Length = 445

 Score = 37.7 bits (86), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 63  LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWRNAC 104
           LP EL   V + + P DL +A+  CR W+    + + WR  C
Sbjct: 22  LPKELALYVLSFLEPKDLLQAAQTCRYWRILAEDNLLWREKC 63


>pdb|3L2O|B Chain B, Structure-Based Mechanism Of Dimerization-Dependent
           Ubiquitination By The Scffbx4 Ubiquitin Ligase
          Length = 312

 Score = 33.9 bits (76), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 63  LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWRNACLK 106
           LP ++   + + +SP+DL +       W  T+R+P+ WR   L+
Sbjct: 8   LPIDVQLYILSFLSPHDLCQLGSTNHYWNETVRDPILWRYFLLR 51


>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 = 33.1 bits (74), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 22/39 (56%)

Query: 63  LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWR 101
           LPDELL  +F+ +   +L K S VC++W     +   W+
Sbjct: 12  LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQ 50


>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 = 32.7 bits (73), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 22/39 (56%)

Query: 63  LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWR 101
           LPDELL  +F+ +   +L K S VC++W     +   W+
Sbjct: 12  LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQ 50


>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 = 32.3 bits (72), Expect = 0.43,   Method: Composition-based stats.
 Identities = 14/39 (35%), Positives = 22/39 (56%)

Query: 63  LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFWR 101
           LPDELL  +F+ +   +L K S VC++W     +   W+
Sbjct: 12  LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLWQ 50


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

 Score = 31.6 bits (70), Expect = 0.60,   Method: Composition-based stats.
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 63  LPDELLFEVFARMSPYDLGKASCVCRKWKYTIRNPVFW 100
           LPDELL  +F+ +   +L K S VC++W     +   W
Sbjct: 4   LPDELLLGIFSCLCLPELLKVSGVCKRWYRLASDESLW 41


  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    0.447 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,393,436
Number of Sequences: 62578
Number of extensions: 436867
Number of successful extensions: 1113
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1107
Number of HSP's gapped (non-prelim): 6
length of query: 337
length of database: 14,973,337
effective HSP length: 99
effective length of query: 238
effective length of database: 8,778,115
effective search space: 2089191370
effective search space used: 2089191370
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)