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= 016055
         (396 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 =  139 bits (349), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 100/362 (27%), Positives = 171/362 (47%), Gaps = 37/362 (10%)

Query: 56  RLLVGYGMGLLSYVVPVYIAEITPKNLRGGFTTVHQLMICIGVSMTYLIGAFL------- 108
           R++ G G+GL S + P+YIAE+ P ++RG   + +Q  I  G  + Y +  F+       
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192

Query: 109 -----NWRILALIGTIPCLVQLIGLCFIPESPRWLAKTGKGIESEAALQRLRGXXXXXXX 163
                 WR +     IP L+ L+ L  +PESPRWL   GK  ++E  L+++ G       
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQA 252

Query: 164 XXXXXXXYTETLER-LSEGGILELFQRKYAHSLIVGVGLMVLQQFGGVNXXXXXXXXXXX 222
                     +L+     GG L +F       +++GV L + QQF G+N           
Sbjct: 253 VQEI----KHSLDHGRKTGGRLLMFG---VGVIVIGVMLSIFQQFVGINVVLYYAPEVFK 305

Query: 223 XXXXXXXXXXXXMV---VIQIPMTLLGVLLMDKSGRRPLLLVSXXXXXXXXXXXXXSFLF 279
                        +   VI +  T+L ++ +DK GR+PL ++              +F  
Sbjct: 306 TLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAF-- 363

Query: 280 QDLQQWIKATPFLALVGVLVYTGSFSLGMGGIPWVIMSEVFPINMKGSAGSLVTLVSWLG 339
                + +A   +AL+ +L Y  +F++  G + WV++SE+FP  ++G A ++     WL 
Sbjct: 364 -----YTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLA 418

Query: 340 SWIISFTFNFLMKWS-------STGTFFAFSAICSLTVLFVAKLVPETKGRTLEEIQASM 392
           ++ +S+TF  + K S       +  +++ +  +  L  LF+ K VPETKG+TLEE++A  
Sbjct: 419 NYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALW 478

Query: 393 NP 394
            P
Sbjct: 479 EP 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
   0.329    0.143    0.457 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,106,766
Number of Sequences: 62578
Number of extensions: 372998
Number of successful extensions: 730
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 723
Number of HSP's gapped (non-prelim): 2
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 bits)