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= 039541
         (521 letters)

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

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 38.9 bits (89), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 46/215 (21%), Positives = 93/215 (43%), Gaps = 36/215 (16%)

Query: 101 DTTIISDWSLECAGSSILSGLPSSCFFIGCLLGGLALSTLGD--SSSLGRKKLLFLSCFA 158
           +T  ++  +L  + ++ L G   +   IGC++GG     LG   S+  GR+  L ++   
Sbjct: 39  NTVFVAPQNLSESAANSLLGFCVASALIGCIIGG----ALGGYCSNRFGRRDSLKIAAVL 94

Query: 159 MSITALATIFA----------NNIWIYSTIRFVAGFFRAPIMTSVIVLLSEMVSKRW--- 205
             I+ + + +           N + +Y    +V  F    I+  + V L+ M+S  +   
Sbjct: 95  FFISGVGSAWPELGFTSINPDNTVPVYLA-GYVPEFVIYRIIGGIGVGLASMLSPMYIAE 153

Query: 206 ------RGQVVIIGFTFFSFGLVSLPAVAYLSRGSS---------WKMLYVWTSIPSIVC 250
                 RG++V        FG + +  V Y    S          W+ ++    IP+++ 
Sbjct: 154 LAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLF 213

Query: 251 CIIIYPFISESPRWLFIHGHEAEAMAVLKRLASRS 285
            +++Y  + ESPRWL   G + +A  +L+++   +
Sbjct: 214 LMLLYT-VPESPRWLMSRGKQEQAEGILRKIMGNT 247


>pdb|2O1X|A Chain A, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
 pdb|2O1X|B Chain B, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
 pdb|2O1X|C Chain C, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
 pdb|2O1X|D Chain D, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
           Deinococcus Radiodurans
          Length = 629

 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 21/34 (61%)

Query: 129 GCLLGGLALSTLGDSSSLGRKKLLFLSCFAMSIT 162
           G L GG+AL+ L     +GRK L+ L+   MSI+
Sbjct: 155 GSLTGGMALAALNTIGDMGRKMLIVLNDNEMSIS 188


  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
   0.326    0.138    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,700,491
Number of Sequences: 62578
Number of extensions: 421837
Number of successful extensions: 893
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 890
Number of HSP's gapped (non-prelim): 3
length of query: 521
length of database: 14,973,337
effective HSP length: 103
effective length of query: 418
effective length of database: 8,527,803
effective search space: 3564621654
effective search space used: 3564621654
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)