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= 011956
         (474 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 =  145 bits (365), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 127/491 (25%), Positives = 212/491 (43%), Gaps = 83/491 (16%)

Query: 41  TFVAVCGSYVFGSAIGYSSPAQSGITNDLGL---------SVAEYSLFGSILT---IGAM 88
           T VA  G  +FG    Y +   SG    L             A  SL G  +    IG +
Sbjct: 14  TLVATLGGLLFG----YDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCI 69

Query: 89  IGAIMSGKIADYIGRRGTMGFSDIVCIIGWVIIVFSKAAWWLDLG--------------- 133
           IG  + G  ++  GRR ++  + ++  I  V       + W +LG               
Sbjct: 70  IGGALGGYCSNRFGRRDSLKIAAVLFFISGV------GSAWPELGFTSINPDNTVPVYLA 123

Query: 134 ---------RLLVGYGMGLLSYVVPVYIAEITPKNLRGGFTTVHQLMICIGVSMTYLIGA 184
                    R++ G G+GL S + P+YIAE+ P ++RG   + +Q  I  G  + Y +  
Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183

Query: 185 FL------------NWRILALIGTIPCLVQLIGLCFIPESPRWLAKTGKGIESEAALQRL 232
           F+             WR +     IP L+ L+ L  +PESPRWL   GK  ++E  L+++
Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI 243

Query: 233 RGXXXXXXXXXXXXXXYTETLER-LSEGGILELFQRKYAHSLIVGVGLMVLQQFGGVNXX 291
            G                 +L+     GG L +F       +++GV L + QQF G+N  
Sbjct: 244 MGNTLATQAVQEI----KHSLDHGRKTGGRLLMFG---VGVIVIGVMLSIFQQFVGINVV 296

Query: 292 XXXXXXXXXXXXXXXXXXXXXMV---VIQIPMTLLGVLLMDKSGRRPLLLVSXXXXXXXX 348
                                 +   VI +  T+L ++ +DK GR+PL ++         
Sbjct: 297 LYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGM 356

Query: 349 XXXXXSFLFQDLQQWIKATPFLALVGVLVYTGSFSLGMGGIPWVIMSEVFPINMKGSAGS 408
                +F       + +A   +AL+ +L Y  +F++  G + WV++SE+FP  ++G A +
Sbjct: 357 FSLGTAF-------YTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALA 409

Query: 409 LVTLVSWLGSWIISFTFNFLMKWS-------STGTFFAFSAICSLTVLFVAKLVPETKGR 461
           +     WL ++ +S+TF  + K S       +  +++ +  +  L  LF+ K VPETKG+
Sbjct: 410 IAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGK 469

Query: 462 TLEEIQASMNP 472
           TLEE++A   P
Sbjct: 470 TLEELEALWEP 480


  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
   0.327    0.142    0.436 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,220,730
Number of Sequences: 62578
Number of extensions: 420312
Number of successful extensions: 901
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: 893
Number of HSP's gapped (non-prelim): 3
length of query: 474
length of database: 14,973,337
effective HSP length: 102
effective length of query: 372
effective length of database: 8,590,381
effective search space: 3195621732
effective search space used: 3195621732
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)