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= 011308
         (489 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 =  150 bits (379), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 130/475 (27%), Positives = 202/475 (42%), Gaps = 48/475 (10%)

Query: 54  LVAIISSFLFGYHLGVVNETLESISL------DLGFSGSTMAEGLVVSTCLGGAFVGSMF 107
           LVA +   LFGY   V++ T+ES++       +L  S +    G  V++ L G  +G   
Sbjct: 15  LVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGAL 74

Query: 108 SGWIADGIGRRRAFQLCALPMIIGASMSA--------------ITKNLWG----MLLGRL 149
            G+ ++  GRR + ++ A+   I    SA              +   L G     ++ R+
Sbjct: 75  GGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRI 134

Query: 150 FVGTGMGIGPAVAALYVSEVSPAYVRGAYGSSTQIAACLGILVALFVG--LPAKEILGW- 206
             G G+G+   ++ +Y++E++PA++RG   S  Q A   G L+   V   +       W 
Sbjct: 135 IGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWL 194

Query: 207 ----WRICFWVATIPAAFLALFMEFCAESPHWLFKXXXXXXXXXXXXXXXXXXHVKYSMA 262
               WR  F    IPA    + +    ESP WL                        ++ 
Sbjct: 195 NTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQ 254

Query: 263 ELSKSERGDEADAVKFSELISPRNFGVVFIGSTLFALQQLSGINAVFYFSSTVFKNAGVP 322
           E+  S         +          GV+ IG  L   QQ  GIN V Y++  VFK  G  
Sbjct: 255 EIKHSLDHGRKTGGRLLMF----GVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGAS 310

Query: 323 SDSG---NICVGIANLSGSIIAMILMDKLGRRVLLLGSFLGMAIAMGVQAIAXXXXXXXX 379
           +D      I VG+ NL+ +++A++ +DK GR+ L +   LGMAI M     +        
Sbjct: 311 TDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGM----FSLGTAFYTQ 366

Query: 380 XXXXXXXXXXXXXXXXFSLGAGPVPSLLLSEIFPNRIRAKAMAVCMAVHWVINFFVG--- 436
                           F++  GPV  +LLSEIFPN IR KA+A+ +A  W+ N+FV    
Sbjct: 367 APGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTF 426

Query: 437 ---XXXXXXXXXXXXXILYTIFGSFCFLAVIYVKRNVMETKGKTLQEIEMALLPQ 488
                             Y I+G    LA +++ + V ETKGKTL+E+E    P+
Sbjct: 427 PMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWEPE 481


  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    0.140    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,729,962
Number of Sequences: 62578
Number of extensions: 425241
Number of successful extensions: 1055
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1046
Number of HSP's gapped (non-prelim): 5
length of query: 489
length of database: 14,973,337
effective HSP length: 103
effective length of query: 386
effective length of database: 8,527,803
effective search space: 3291731958
effective search space used: 3291731958
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: 53 (25.0 bits)