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= psy8366
         (513 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 = 89.7 bits (221), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 109/484 (22%), Positives = 205/484 (42%), Gaps = 73/484 (15%)

Query: 48  GMAFGMPTVVVGVLDHKVASNQTILESPDLILSDEQSSWLG---SILFLFHPFGSIISGY 104
           G+ FG  T V+      V S  T+  +P  +     +S LG   +   +    G  + GY
Sbjct: 21  GLLFGYDTAVI---SGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGY 77

Query: 105 FLEYIGRKRLMILVGFPFFL-----GW-------------ILLYLAETVSIIMLGTVCMG 146
                GR+  + +    FF+      W             + +YLA  V   ++  +  G
Sbjct: 78  CSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIGG 137

Query: 147 LSVGCCEAPIISYIGEISEPRMRGSLSLFAGAACNFGVFIIFLI-----------YALTD 195
           + VG        YI E++   +RG L  F   A  FG  +++ +           +  TD
Sbjct: 138 IGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTD 197

Query: 196 -WRTTVLISAIFPILTMIMIAFIPESPTWLVSKGRLEEAERSLRWVRGWSKKHKVRVEFE 254
            WR       I  +L ++++  +PESP WL+S+G+ E+AE  LR + G            
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMG------------ 245

Query: 255 QLVKDTNSATLYVADSEYTTDQRKSSQLSKLLNYLVRPEIVRPXXXXXXXXXXXXXASLQ 314
                   AT  V + +++ D  + +   +LL + V   ++                 + 
Sbjct: 246 -----NTLATQAVQEIKHSLDHGRKTG-GRLLMFGVGVIVIG-----VMLSIFQQFVGIN 294

Query: 315 PMRPFLVEIFRTFGLPMKSEWV-LVLTGILSITGSFVSTITVNKLGKRGMTLWSTGINTF 373
            +  +  E+F+T G       +  ++ G++++T + ++ +TV+K G++ + +   G    
Sbjct: 295 VVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQI--IGALGM 352

Query: 374 FTLMLSI-CAMNLQWPGWIPLTIFCTCFWVSGYGML--PLPWMLLSEVFPLQVRXXXXXX 430
              M S+  A   Q PG + L      F+V+ + M   P+ W+LLSE+FP  +R      
Sbjct: 353 AIGMFSLGTAFYTQAPGIVAL--LSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAI 410

Query: 431 XXXXXXVVNFISTKTY--INLTSWFGLHG----TLFIYTLVSFLGFIYIYFYVPETEDRT 484
                 + N+  + T+  ++  SW   H     + +IY  +  L  ++++ +VPET+ +T
Sbjct: 411 AVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKT 470

Query: 485 LQEI 488
           L+E+
Sbjct: 471 LEEL 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
   0.326    0.140    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,283,397
Number of Sequences: 62578
Number of extensions: 488506
Number of successful extensions: 1485
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1480
Number of HSP's gapped (non-prelim): 2
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
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: 54 (25.4 bits)