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= 045590
         (261 letters)

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

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



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

 Score = 32.3 bits (72), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 23/125 (18%)

Query: 6   LPEDCFAHILSYTSPRDACRLSLVSSTVRFAADSDNVWEKFL--------PVDY-----M 52
           LP D   +ILS+ SP D C+L   +           +W  FL         VD+     +
Sbjct: 8   LPIDVQLYILSFLSPHDLCQLGSTNHYWNETVRDPILWRYFLLRDLPSWSSVDWKSLPDL 67

Query: 53  EILPRLVLPL---VYFSKKELFMRLCSPVLIDQGKKTFSL------EKSTSKKRYILGAR 103
           EIL + +  +    +F    ++ R+C P LI Q +  F++      E +TS    ++ + 
Sbjct: 68  EILKKPISEVTDGAFFDYMAVY-RMCCPYLIIQNEPRFAMFGPGLEELNTSLVLSLMSSE 126

Query: 104 ELSIT 108
           EL  T
Sbjct: 127 ELCPT 131


>pdb|1V92|A Chain A, Solution Structure Of The Uba Domain From P47, A Major
           Cofactor Of The Aaa Atpase P97
          Length = 46

 Score = 28.1 bits (61), Expect = 5.5,   Method: Composition-based stats.
 Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 6/43 (13%)

Query: 214 RDEALRSRVS----EGDGERFAREREDGW-IEIELGSFYNDGG 251
           R +ALR  V+    E D  RF  E   GW ++I L SFY DGG
Sbjct: 5   RQDALREFVAVTGAEEDRARFFLESA-GWDLQIALASFYEDGG 46


  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
   0.320    0.136    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,013,070
Number of Sequences: 62578
Number of extensions: 317194
Number of successful extensions: 708
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 708
Number of HSP's gapped (non-prelim): 3
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
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: 50 (23.9 bits)