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= 038777
         (361 letters)

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

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



>pdb|1VBG|A Chain A, Pyruvate Phosphate Dikinase From Maize
 pdb|1VBH|A Chain A, Pyruvate Phosphate Dikinase With Bound Mg-Pep From Maize
          Length = 876

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 19/32 (59%)

Query: 288 LLKGQQTDRVDAILQPEELEVMDNVLPAKYEE 319
           L+  Q  D V  I  PE+L+ M N++P  Y+E
Sbjct: 276 LVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDE 307


>pdb|3UVV|A Chain A, Crystal Structure Of The Ligand Binding Domains Of The
          Thyroid Receptor:retinoid X Receptor Complexed With
          3,3',5 Triiodo-L- Thyronine And 9-Cis Retinoic Acid
          Length = 265

 Score = 28.1 bits (61), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 3/39 (7%)

Query: 43 VFLKAYRNTVPVPRHWCQKRKFLQGKRGIGKQPF-HLPD 80
          V  +A+R+T     HW QKRKFL     IG+ P   +PD
Sbjct: 25 VVTEAHRSTNAQGSHWKQKRKFL--PEDIGQSPMASMPD 61


  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
   0.316    0.134    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,838,583
Number of Sequences: 62578
Number of extensions: 393085
Number of successful extensions: 844
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 842
Number of HSP's gapped (non-prelim): 7
length of query: 361
length of database: 14,973,337
effective HSP length: 100
effective length of query: 261
effective length of database: 8,715,537
effective search space: 2274755157
effective search space used: 2274755157
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)