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= 010212
         (515 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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 105/510 (20%), Positives = 184/510 (36%), Gaps = 80/510 (15%)

Query: 20  YHFTAIVIAGMGFFTDAYDLFCISLVTKLLGRIYYYKEGSDSPGTLPDNVASAVNG---- 75
           Y F+  ++A +G     YD   IS   + L  ++       +P  L ++ A+++ G    
Sbjct: 9   YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFV------APQNLSESAANSLLGFCVA 62

Query: 76  VALCGTLAGQLFFGWLGDKMGRKRVYGMTLMMMVICSLAS-----GLSFGKEPKAVMITL 130
            AL G + G    G+  ++ GR+    +  ++  I  + S     G +       V + L
Sbjct: 63  SALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYL 122

Query: 131 C-------FFRFWLGFGIGGDYPLSATIMSEYANKKTRGAFIAAVFAMQGFGILSGGMVA 183
                    +R   G G+G    LS   ++E A    RG  ++       F I+ G ++ 
Sbjct: 123 AGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVS----FNQFAIIFGQLL- 177

Query: 184 IIVSAAFKANFPAPIYSANPAASTVPEADYI----WRIILMFGAIPALLTYYWRMKMPET 239
                         +Y  N   +   +A ++    WR +     IPALL       +PE+
Sbjct: 178 --------------VYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPES 223

Query: 240 ARY--TXXXXXXXXXXXXDMSXXXXXXXXXXXXXXXXXXGKNDFGLFSAKFVRRHGLHLI 297
            R+  +             +                   G+   G      +   G+ +I
Sbjct: 224 PRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRL---LMFGVGVIVI 280

Query: 298 GTTVTWFLLDVAYYSQNLFQKDIFTAIGWIPKAKTMNAIEEVYKIARAQTLIALCSTVPG 357
           G  ++ F   V       +  ++F  +G    A T         IA  QT+I     +  
Sbjct: 281 GVMLSIFQQFVGINVVLYYAPEVFKTLG----AST--------DIALLQTIIVGVINLTF 328

Query: 358 YWFTVALIDKIGRFAIQLMGFFFMTVFMFALAIPYHHWTLPDHRIGFVVLYSLTFFFSNF 417
               +  +DK GR  +Q++G   M + MF+L   ++         G V L S+ F+ + F
Sbjct: 329 TVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFY-----TQAPGIVALLSMLFYVAAF 383

Query: 418 ----GPNTTTFVVPAEIFPARLRSTCHXXXXXXXXXXXXXXXFGFLYLADTSGVKK---- 469
               GP    +V+ +EIFP  +R                   + F  +   S +      
Sbjct: 384 AMSWGP--VCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHN 441

Query: 470 --ALLILGGANFLGMLFTF-LVPESKGKSL 496
             +  I G    L  LF +  VPE+KGK+L
Sbjct: 442 GFSYWIYGCMGVLAALFMWKFVPETKGKTL 471


  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    0.142    0.449 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,079,123
Number of Sequences: 62578
Number of extensions: 477085
Number of successful extensions: 1018
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1015
Number of HSP's gapped (non-prelim): 6
length of query: 515
length of database: 14,973,337
effective HSP length: 103
effective length of query: 412
effective length of database: 8,527,803
effective search space: 3513454836
effective search space used: 3513454836
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: 54 (25.4 bits)