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= 008603
         (560 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


  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
   0.320    0.138    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,456,500
Number of Sequences: 62578
Number of extensions: 600835
Number of successful extensions: 1163
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1157
Number of HSP's gapped (non-prelim): 5
length of query: 560
length of database: 14,973,337
effective HSP length: 104
effective length of query: 456
effective length of database: 8,465,225
effective search space: 3860142600
effective search space used: 3860142600
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)