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= 011565
         (483 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 =  135 bits (339), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 124/477 (25%), Positives = 208/477 (43%), Gaps = 63/477 (13%)

Query: 52  TLVAVSGSYSFGTGVGYSSPTQNAIR------EDLSLSLAEYSVFGSILT---FGAMIGA 102
           TLVA  G   FG      S T  ++       ++LS S A  S+ G  +     G +IG 
Sbjct: 14  TLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAAN-SLLGFCVASALIGCIIGG 72

Query: 103 ITSGPIADFIGRKGAMRVSS---FVCIAG--W-------------LAIYFSEGALSLDLG 144
              G  ++  GR+ ++++++   F+   G  W             + +Y +       + 
Sbjct: 73  ALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIY 132

Query: 145 RLATGYGMGIFSYVVPVFTAEIAPKELRGALTSANQLLIVIGASTFFIIG---------- 194
           R+  G G+G+ S + P++ AE+AP  +RG L S NQ  I+ G    + +           
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192

Query: 195 --TVATWRTLALVGVIPCAVLLLGLFLIPESPRWLAKIGKHEEFEAALQKLRGKDADISQ 252
                 WR +     IP  + L+ L+ +PESPRWL   GK E+ E  L+K+ G +   +Q
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMG-NTLATQ 251

Query: 253 EATEIQEYIETLERLPKARLLDLFQKRYLHSVTIGVGLMVIQQXXXXXXXXXXXXXXXQT 312
              EI+  ++   R    RLL +F    +  + IGV L + QQ               +T
Sbjct: 252 AVQEIKHSLDH-GRKTGGRLL-MFG---VGVIVIGVMLSIFQQFVGINVVLYYAPEVFKT 306

Query: 313 AGLSPSTG---TISYALLQVVVTFFNIIMIDRAGRKPXXXXXXXXXXXXXXXXXXXXXXK 369
            G S       TI   ++ +  T   I+ +D+ GRKP                      +
Sbjct: 307 LGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQ 366

Query: 370 TYGLALESVPALTLAGVLVYIGSFSSGMGATPWVLMSEIFPINIKGVGGSLTTLVNWFGA 429
             G+       + L  +L Y+ +F+   G   WVL+SEIFP  I+G   ++     W   
Sbjct: 367 APGI-------VALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419

Query: 430 WAISYTFNFLE--TW-----SSYGTFLLYAAVNILGIVFITTVVPETKGRTLEEIQA 479
           + +S+TF  ++  +W      +  ++ +Y  + +L  +F+   VPETKG+TLEE++A
Sbjct: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEA 476


  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
   0.322    0.137    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,964,860
Number of Sequences: 62578
Number of extensions: 442685
Number of successful extensions: 1037
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1030
Number of HSP's gapped (non-prelim): 5
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
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)