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= 001071
         (1165 letters)

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

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



>pdb|4HG6|A Chain A, Structure Of A Cellulose Synthase - Cellulose
           Translocation Intermediate
          Length = 802

 Score = 58.5 bits (140), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 58/123 (47%), Gaps = 4/123 (3%)

Query: 859 GWIYGSVTEDVVTGYRMHNRGWRSVYCVTKRDAFRGTAPINLTDRLHQVLRWATGSVEIF 918
           G+   ++TED  T   +H+RGW+S+Y    R    G  P      + Q  RWATG +++ 
Sbjct: 334 GFAGETITEDAETALEIHSRGWKSLYI--DRAMIAGLQPETFASFIQQRGRWATGMMQML 391

Query: 919 FSRNNALLASRRMKFLQRVAYFNVGMYPFTSMFLLVYCILPAVSLFSGQFIVQSLSISFL 978
             +N   L  R +   QR+ Y N   + F  +  +++ + P + LF G  I  +     L
Sbjct: 392 LLKNP--LFRRGLGIAQRLCYLNSMSFWFFPLVRMMFLVAPLIYLFFGIEIFVATFEEVL 449

Query: 979 IYL 981
            Y+
Sbjct: 450 AYM 452


>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
          Length = 52

 Score = 40.0 bits (92), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 165 CDCGFKICRECYLECAGNGGGRCPGCKEPYKD 196
           C CG++ICR C+     +  G CP C++PY +
Sbjct: 20  CTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51


>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
          Length = 78

 Score = 35.0 bits (79), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 165 CDCGFKICRECYLECAGNGGGRCPGCKEPYKD 196
           C CG++ICR C+     +  G CP C++PY +
Sbjct: 31  CTCGYQICRFCWHRIRTDENGLCPACRKPYPE 62


>pdb|2YHN|A Chain A, The Idol-Ube2d Complex Mediates Sterol-Dependent
           Degradation Of The Ldl Receptor
 pdb|2YHN|B Chain B, The Idol-Ube2d Complex Mediates Sterol-Dependent
           Degradation Of The Ldl Receptor
 pdb|2YHO|A Chain A, The Idol-Ube2d Complex Mediates Sterol-Dependent
           Degradation Of The Ldl Receptor
 pdb|2YHO|C Chain C, The Idol-Ube2d Complex Mediates Sterol-Dependent
           Degradation Of The Ldl Receptor
 pdb|2YHO|E Chain E, The Idol-Ube2d Complex Mediates Sterol-Dependent
           Degradation Of The Ldl Receptor
 pdb|2YHO|G Chain G, The Idol-Ube2d Complex Mediates Sterol-Dependent
           Degradation Of The Ldl Receptor
          Length = 79

 Score = 30.8 bits (68), Expect = 4.5,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 5/52 (9%)

Query: 140 EQTEPVKSGLICGMKGCDEKVMQNKCDCGFKICRECYLECAGNGGGRCPGCK 191
           E+   +K  ++C M  C+E++    C CG  +C E    CA      CP C+
Sbjct: 10  EKLRKLKEAMLC-MVCCEEEINSTFCPCGHTVCCE---SCAAQLQS-CPVCR 56


>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
           Motif Protein 32
          Length = 88

 Score = 30.8 bits (68), Expect = 4.8,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 150 ICGMKGCDEKVMQNKCDCGFKICRECY--LECAGNGGGRCPGCKEPYKDASDGEIEDEV 206
           IC     +E++      CG  ICR+C   L  +   G RCP C +  +  S  ++ D +
Sbjct: 20  ICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLTQLTDNL 78


  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    0.138    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 34,505,663
Number of Sequences: 62578
Number of extensions: 1468352
Number of successful extensions: 2886
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2880
Number of HSP's gapped (non-prelim): 8
length of query: 1165
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1056
effective length of database: 8,152,335
effective search space: 8608865760
effective search space used: 8608865760
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (26.6 bits)