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= 014616
         (421 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 =  134 bits (338), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 118/437 (27%), Positives = 183/437 (41%), Gaps = 58/437 (13%)

Query: 2   ALVGAIVGAASGGWINDAYGRKKATLLADVVFTAGAI--------IMAAAPDPYXXXXXX 53
           AL+G I+G A GG+ ++ +GR+ +  +A V+F    +          +  PD        
Sbjct: 64  ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLA 123

Query: 54  XXXXXXXX----------XASVTAPVYIAEASPSEVRGGLVSTNVLMITSGQFLSYLVNL 103
                              AS+ +P+YIAE +P+ +RG LVS N   I  GQ L Y VN 
Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183

Query: 104 AFTEVPGT--------WRWMLGVSAVPAIIQFVLMLFMPESPRWLFMKSDKEKAILVLSK 155
            F    G         WR+M     +PA++  +L+  +PESPRWL  +  +E+A  +L K
Sbjct: 184 -FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRK 242

Query: 156 IYDIARLEDEIDHLSAAAEEELRK-----KKTVRYLDVFKSKEIRXXXXXXXXXXXXXXX 210
           I          + L+  A +E++      +KT   L +F    I                
Sbjct: 243 IMG--------NTLATQAVQEIKHSLDHGRKTGGRLLMFGVGVI----VIGVMLSIFQQF 290

Query: 211 XXINTVMYYSPTIVQMAGFQSNQXXXXXXXXXXGTNAVGTIVGIYLIDHFGRKKLALSSL 270
             IN V+YY+P + +  G  S              N   T++ I  +D FGRK L +   
Sbjct: 291 VGINVVLYYAPEVFKTLG-ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGA 349

Query: 271 AGVIISLVLLSWAFIXXXXXXXXXVYGWIAVIGLALYIAFFAPGMGPVPWTLNSEVYPEQ 330
            G+ I +  L  AF            G +A++ +  Y+A FA   GPV W L SE++P  
Sbjct: 350 LGMAIGMFSLGTAFYTQAP-------GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNA 402

Query: 331 YRGICGGMSATVNWISNLIVAQTFLTVAE---LVG---TGATXXXXXXXXXXXXXXXXXX 384
            RG    ++    W++N  V+ TF  + +   LV     G +                  
Sbjct: 403 IRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKF 462

Query: 385 XPETQGLTFLEVEQMWK 401
            PET+G T  E+E +W+
Sbjct: 463 VPETKGKTLEELEALWE 479


  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
   0.321    0.135    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,700,822
Number of Sequences: 62578
Number of extensions: 312402
Number of successful extensions: 600
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: 592
Number of HSP's gapped (non-prelim): 5
length of query: 421
length of database: 14,973,337
effective HSP length: 101
effective length of query: 320
effective length of database: 8,652,959
effective search space: 2768946880
effective search space used: 2768946880
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)