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= 029336
         (195 letters)

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

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



>pdb|4FE7|A Chain A, Structure Of Xylose-binding Transcription Activator Xylr
          Length = 412

 Score = 28.1 bits (61), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 113 RLDKFSSWLRDHVVDSKNWNKIRACLADTDT 143
           R+DK   WL D V+   +  +I   LAD D 
Sbjct: 68  RIDKIKDWLGDGVIADFDDKQIEQALADVDV 98


>pdb|4FE4|A Chain A, Crystal Structure Of Apo E. Coli Xylr
 pdb|4FE4|B Chain B, Crystal Structure Of Apo E. Coli Xylr
 pdb|4FE4|C Chain C, Crystal Structure Of Apo E. Coli Xylr
          Length = 392

 Score = 28.1 bits (61), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 113 RLDKFSSWLRDHVVDSKNWNKIRACLADTDT 143
           R+DK   WL D V+   +  +I   LAD D 
Sbjct: 48  RIDKIKDWLGDGVIADFDDKQIEQALADVDV 78


>pdb|3IIE|A Chain A, 1-deoxy-d-xylulose 5-phosphate Reductoisomerase From
           Yersinia Pestis.
 pdb|3IIE|B Chain B, 1-deoxy-d-xylulose 5-phosphate Reductoisomerase From
           Yersinia Pestis
          Length = 401

 Score = 26.6 bits (57), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 15/55 (27%), Positives = 23/55 (41%)

Query: 106 GRAYKEYRLDKFSSWLRDHVVDSKNWNKIRACLADTDTCSKLSQQYVTADQFFSA 160
           G  ++E  L +FS    D      NW+  R    D+ T      +Y+ A   F+A
Sbjct: 190 GGPFRETPLSQFSDVTPDQACAHPNWSMGRKISVDSATMMNKGLEYIEARWLFNA 244


  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
   0.324    0.135    0.445 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,010,348
Number of Sequences: 62578
Number of extensions: 160659
Number of successful extensions: 333
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 330
Number of HSP's gapped (non-prelim): 3
length of query: 195
length of database: 14,973,337
effective HSP length: 94
effective length of query: 101
effective length of database: 9,091,005
effective search space: 918191505
effective search space used: 918191505
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)