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= psy13784
         (388 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 = 79.0 bits (193), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 83/379 (21%), Positives = 156/379 (41%), Gaps = 66/379 (17%)

Query: 35  IGRFLTGVSEGLSASPATIYIAESIMVQNTKLRGSLATWATTARAFGLLQVYFMGSLLR- 93
           I R + G+  GL++  + +YIAE   +    +RG L ++   A  FG L VY +   +  
Sbjct: 131 IYRIIGGIGVGLASMLSPMYIAE---LAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIAR 187

Query: 94  -----------YRKVAAMAAIFSALGTILITFIIPESPAWLNSKGRRGDAEWAAKRLRLG 142
                      +R + A   I  AL  +++ + +PESP WL S+G++  AE   +++   
Sbjct: 188 SGDASWLNTDGWRYMFASECI-PALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246

Query: 143 PPSNQTEPTSRGDAESGAQ-GEQM-----------STTNIFKEFMKPEAYKPXXXXXXXX 190
             + Q     +   + G + G ++              +IF++F+               
Sbjct: 247 TLATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFV--------------- 291

Query: 191 XXXXXXAVNVILAYMTDFVRSSGFHLLNPYFITVIGGLXXXXXXXXXXXXLPHTGVKPLS 250
                  +NV+L Y  +  ++ G         T+I G+            +   G KPL 
Sbjct: 292 ------GINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQ 345

Query: 251 AASGMGIALSMLVIGTYLLFEKAPIVNFEWGFFNLIPXXXXXXXXXXXXXGFLPIPYLML 310
               +G+A+ M  +GT   + +AP          ++               + P+ +++L
Sbjct: 346 IIGALGMAIGMFSLGT-AFYTQAP---------GIVALLSMLFYVAAFAMSWGPVCWVLL 395

Query: 311 GEIFPMEVKGVAAGLATCLAYIFGFFAVKTWPTLH------LALGNGI-FFFYGLVAAIG 363
            EIFP  ++G A  +A    ++  +F   T+P +           NG  ++ YG +  + 
Sbjct: 396 SEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLA 455

Query: 364 TAHVLAYLPETKGKSLEEI 382
              +  ++PETKGK+LEE+
Sbjct: 456 ALFMWKFVPETKGKTLEEL 474


  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    0.139    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,348,534
Number of Sequences: 62578
Number of extensions: 330660
Number of successful extensions: 493
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 488
Number of HSP's gapped (non-prelim): 3
length of query: 388
length of database: 14,973,337
effective HSP length: 101
effective length of query: 287
effective length of database: 8,652,959
effective search space: 2483399233
effective search space used: 2483399233
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: 52 (24.6 bits)