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= 013304
         (446 letters)

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

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



>pdb|3UV4|A Chain A, Crystal Structure Of The Second Bromodomain Of Human
           Transcription Initiation Factor Tfiid Subunit 1 (Taf1)
 pdb|3UV4|B Chain B, Crystal Structure Of The Second Bromodomain Of Human
           Transcription Initiation Factor Tfiid Subunit 1 (Taf1)
          Length = 158

 Score = 31.6 bits (70), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 26/123 (21%), Positives = 53/123 (43%), Gaps = 9/123 (7%)

Query: 229 SSGADDQSGSLRKDSIDDIKGVFESVAQN---------ESAFVFRHRLDSQKRGRYKKMI 279
           SSG D  + +L   S+DD +  F  +  N           ++ F H ++ +    Y K+I
Sbjct: 8   SSGVDLGTENLYFQSMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVI 67

Query: 280 LRHMDVDTXXXXXXXXXXXXXKELFRDLLLLANNAVVFYSKNTREHKSAFLLRTIVLKTM 339
           +  MD++T             +    D+ L+  N+V +    ++  K+A  +  +  +T+
Sbjct: 68  VNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTL 127

Query: 340 RQY 342
            +Y
Sbjct: 128 TEY 130


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

 Score = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 215 RKENSTPVSGQFARSSGADDQSGSLRKDSIDDIKGVFESVAQNESAFVFRHRLDSQKRGR 274
           R+E+++ V+  F+R +  DDQ GS R   I  I+ V E V      F++    ++ KR  
Sbjct: 173 REEHTSAVNKMFSRHNEGDDQQGS-RYSVIPQIQKVCEVV----DGFIYVANAEAHKRHE 227

Query: 275 YK 276
           ++
Sbjct: 228 WQ 229


>pdb|3IU5|A Chain A, Crystal Structure Of The First Bromodomain Of Human
           Poly-Bromodomain Containing Protein 1 (Pb1)
          Length = 116

 Score = 28.9 bits (63), Expect = 5.8,   Method: Composition-based stats.
 Identities = 15/45 (33%), Positives = 25/45 (55%)

Query: 303 LFRDLLLLANNAVVFYSKNTREHKSAFLLRTIVLKTMRQYFKDNE 347
           L  D  LL NNA  +Y  ++ E+K+A  L  + L+T  ++ +  E
Sbjct: 72  LTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQKGE 116


  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
   0.314    0.128    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,954,824
Number of Sequences: 62578
Number of extensions: 387818
Number of successful extensions: 587
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 583
Number of HSP's gapped (non-prelim): 9
length of query: 446
length of database: 14,973,337
effective HSP length: 102
effective length of query: 344
effective length of database: 8,590,381
effective search space: 2955091064
effective search space used: 2955091064
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)