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= 023639
         (279 letters)

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

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



>pdb|1S1Q|A Chain A, Tsg101(Uev) Domain In Complex With Ubiquitin
 pdb|1S1Q|C Chain C, Tsg101(Uev) Domain In Complex With Ubiquitin
          Length = 145

 Score = 28.5 bits (62), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 170 DYTVQDQNELTSMETEIETFLSSPVDNESSSDIDNPNAGSVPAPSGGNFSSVNETIWEDF 229
           D TV++   + ++  +++  L S V N+ SS       G++P P  GN  ++   +W   
Sbjct: 19  DLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELXNLTGTIPVPYRGNTYNIPICLW--- 75

Query: 230 MADDLIAGDPEEVVVKDQSEAEVE 253
              D    +P    VK  S   ++
Sbjct: 76  -LLDTYPYNPPICFVKPTSSXTIK 98


>pdb|2LDU|A Chain A, Solution Nmr Structure Of Heat Shock Factor Protein 1 Dna
           Binding Domain From Homo Sapiens, Northeast Structural
           Genomics Consortium Target Hr3023c
          Length = 125

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 11/44 (25%)

Query: 1   MQGFRKV---------DPDR--WEFANEGFLGGQKHLLKTIKRR 33
           M GFRKV          P+R   EF +  FL GQ+ LL+ IKR+
Sbjct: 77  MYGFRKVVHIEQGGLVKPERDDTEFQHPCFLRGQEQLLENIKRK 120


  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
   0.313    0.130    0.367 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,134,682
Number of Sequences: 62578
Number of extensions: 317557
Number of successful extensions: 711
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 706
Number of HSP's gapped (non-prelim): 12
length of query: 279
length of database: 14,973,337
effective HSP length: 98
effective length of query: 181
effective length of database: 8,840,693
effective search space: 1600165433
effective search space used: 1600165433
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)