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= psy11547
         (587 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 =  156 bits (395), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 119/485 (24%), Positives = 215/485 (44%), Gaps = 62/485 (12%)

Query: 103 GMVFGFSAAATSQLISR-----DSPYRITSDESTWIASLSAIGTMVGCV----LGGYMMD 153
           G++FG+  A  S  +        +P  ++   +  +        ++GC+    LGGY  +
Sbjct: 21  GLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSN 80

Query: 154 LVGRKMTLIITEVPTIL-----GWALIALAPSLPSSILPWIFTG--------RILTGLGS 200
             GR+ +L I  V   +      W  +      P + +P    G        RI+ G+G 
Sbjct: 81  RFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIGGIGV 140

Query: 201 GMVGAPSRIYTAECSQPHLRGMLSSLASFGVSLGVLFEYSLGAFLS------------WD 248
           G+    S +Y AE +  H+RG L S   F +  G L  Y +  F++            W 
Sbjct: 141 GLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWR 200

Query: 249 TVAAISTIIPVLSIIAGCLMPESPSWLLSQGRKDACRNSLRRLRANNYDVEKEVQGLYEF 308
            + A   I  +L ++    +PESP WL+S+G+++     LR++  N    +         
Sbjct: 201 YMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQA-------- 252

Query: 309 SKRQETQKSRNFKETLAAIVEPACLKPFVILMLYFLIYQFSGVNPVTFYAVNIFKDAGAH 368
              QE + S +        +    +   VI ++  +  QF G+N V +YA  +FK  GA 
Sbjct: 253 --VQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGAS 310

Query: 369 VNNNL-AAVIMGIVRLIFTIASCIMMKKMGRRSLTFISSIGCGVSMTGLGLYIFATKDFW 427
            +  L   +I+G++ L FT+ + + + K GR+ L  I ++G  + M  LG   +      
Sbjct: 311 TDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQA--- 367

Query: 428 PEYKFPAFVSYLPVLMLMTFTAASTIGYLVVPWVMIGEVYPTKVRGIVGGLTTCA---CH 484
                P  V+ L +L    + AA  + +  V WV++ E++P  +RG    +   A    +
Sbjct: 368 -----PGIVALLSMLF---YVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419

Query: 485 FFI---FLTVKSYNMFQTHLTKEGTFLMYGCISLLGTIFFYVYLPETKNKTLQEIEEQFA 541
           +F+   F  +   +    H     ++ +YGC+ +L  +F + ++PETK KTL+E+E  + 
Sbjct: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479

Query: 542 GKSKK 546
            ++KK
Sbjct: 480 PETKK 484


  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
   0.323    0.137    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,173,671
Number of Sequences: 62578
Number of extensions: 639083
Number of successful extensions: 1172
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1163
Number of HSP's gapped (non-prelim): 6
length of query: 587
length of database: 14,973,337
effective HSP length: 104
effective length of query: 483
effective length of database: 8,465,225
effective search space: 4088703675
effective search space used: 4088703675
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)