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= 041889
         (350 letters)

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

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



>pdb|1LDK|A Chain A, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
           Ligase Complex
          Length = 396

 Score = 28.5 bits (62), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 173 QPFLADGLQYTHDEFVELLISTLNQQFSRLYQLGARKLVMHGLGPL 218
           Q  +   L+  H EF  LL +  N+   R+Y L +R  +  GLG L
Sbjct: 279 QVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSR--IQDGLGEL 322


>pdb|1LDJ|A Chain A, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
           Ligase Complex
          Length = 760

 Score = 28.5 bits (62), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 173 QPFLADGLQYTHDEFVELLISTLNQQFSRLYQLGARKLVMHGLGPL 218
           Q  +   L+  H EF  LL +  N+   R+Y L +R  +  GLG L
Sbjct: 277 QVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSR--IQDGLGEL 320


>pdb|1U6G|A Chain A, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
          Length = 776

 Score = 28.1 bits (61), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 173 QPFLADGLQYTHDEFVELLISTLNQQFSRLYQLGARKLVMHGLGPL 218
           Q  +   L+  H EF  LL +  N+   R+Y L +R  +  GLG L
Sbjct: 293 QVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSR--IQDGLGEL 336


>pdb|1U5F|A Chain A, Crystal Structure Of The Ph Domain Of Skap-Hom With 8
           Vector-Derived N-Terminal Residues
          Length = 148

 Score = 27.7 bits (60), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 7/63 (11%)

Query: 220 CIPSQRVKSKKGQCLKRVNEWIQEFNSKAQELVETLNGRLPSAQFLFADTYSDVYDLIDH 279
           C P +R+        K   EW+Q+     Q+L   +   +P       +   ++YD +DH
Sbjct: 90  CAPDKRIYQFTAASPKDAEEWVQQLKFILQDLGSDV---IPEDD----EERGELYDDVDH 142

Query: 280 PTA 282
           P A
Sbjct: 143 PAA 145


  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
   0.318    0.135    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,624,642
Number of Sequences: 62578
Number of extensions: 444234
Number of successful extensions: 1086
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1084
Number of HSP's gapped (non-prelim): 9
length of query: 350
length of database: 14,973,337
effective HSP length: 100
effective length of query: 250
effective length of database: 8,715,537
effective search space: 2178884250
effective search space used: 2178884250
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)