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= 004750
         (732 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 =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 70/223 (31%), Positives = 113/223 (50%), Gaps = 31/223 (13%)

Query: 19  GWDNATIAGAVLYIKREF------HLETEPTIEGLIVAMSLIGATCITTCSGAIADWLGR 72
           G+D A I+G V  +   F            ++ G  VA +LIG        G  ++  GR
Sbjct: 25  GYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSNRFGR 84

Query: 73  RPMLIVSSVLYFIGGLVMLW--------SPN----VYV------LLLARLLDGFGIGLAV 114
           R  L +++VL+FI G+   W        +P+    VY+       ++ R++ G G+GLA 
Sbjct: 85  RDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIGGIGVGLAS 144

Query: 115 TLVPIYISETAPPEIRGLLNTLPQFTGCVGMFLAYCMVFGM------SLMTAPSWRLMLG 168
            L P+YI+E AP  IRG L +  QF    G  L YC+ + +      S +    WR M  
Sbjct: 145 MLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFA 204

Query: 169 VLFIPSLIYFVLTIFYLPESPRWLVSKGRMLEAKKVLQSLRGR 211
              IP+L+ F++ ++ +PESPRWL+S+G+  +A+ +L+ + G 
Sbjct: 205 SECIPALL-FLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246



 Score = 70.1 bits (170), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 56/218 (25%), Positives = 92/218 (42%), Gaps = 27/218 (12%)

Query: 509 RALMVGVGI-------QILQQLSGINGVLYYTPQILEQAGVGVXXXXXXXXXXXXXXXXX 561
           R LM GVG+        I QQ  GIN VLYY P++ +  G                    
Sbjct: 269 RLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQTII-------- 320

Query: 562 XXTTLLMLPSIAVAMRLMDISGRRXXXXXXXXXXXXXXXXXXXXXXXKMGSVVHASISTV 621
               ++ L    +A+  +D  GR+                       +   +V    + +
Sbjct: 321 --VGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIV----ALL 374

Query: 622 SVVLYFCCFVMGFGPIPNILCSEIFPTRVRGICIAICALVFWIGDIIVTYSLPVLLNSVG 681
           S++ Y   F M +GP+  +L SEIFP  +RG  +AI     W+ +  V+++ P++  +  
Sbjct: 375 SMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSW 434

Query: 682 LAGVFG------MYAVVCVISWIFVFIKVPETKGMPLE 713
           L   F       +Y  + V++ +F++  VPETKG  LE
Sbjct: 435 LVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLE 472


  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    0.139    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,756,231
Number of Sequences: 62578
Number of extensions: 721671
Number of successful extensions: 1271
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: 1262
Number of HSP's gapped (non-prelim): 6
length of query: 732
length of database: 14,973,337
effective HSP length: 106
effective length of query: 626
effective length of database: 8,340,069
effective search space: 5220883194
effective search space used: 5220883194
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: 55 (25.8 bits)