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= psy3807
         (483 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 = 86.3 bits (212), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 74/283 (26%), Positives = 127/283 (44%), Gaps = 27/283 (9%)

Query: 210 RGGLGTVNQLAVTLGLLISQIL-------GIEPILGTDEGWPVLLAMLGMFQFGYNTGVI 262
           RG L + NQ A+  G L+   +       G    L TD GW  + A   +    +   + 
Sbjct: 160 RGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTD-GWRYMFASECIPALLFLMLLY 218

Query: 263 NAPEKVTLRKLRAST-QIEVDIEEMRVEQIAQQSESKISMSELLCSSTLRKPL------- 314
             PE       R    Q E  + ++    +A Q+  +I  S      T  + L       
Sbjct: 219 TVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVGVI 278

Query: 315 IIGIVMQLSQQFSGINAVFYYSTALFESSGLSEKTAKFTTIGIGAVMVTMTIISIPLMDR 374
           +IG+++ + QQF GIN V YY+  +F++ G S   A   TI +G + +T T+++I  +D+
Sbjct: 279 VIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDK 338

Query: 375 MGRRTLHLYGLGGMXXXXXXXXXXXXXKEFFGFVQEMIDWMSYLSVISILGFVVFFAVGP 434
            GR+ L + G  GM             +               ++++S+L +V  FA+  
Sbjct: 339 FGRKPLQIIGALGMAIGMFSLGTAFYTQA-----------PGIVALLSMLFYVAAFAMSW 387

Query: 435 GSIPWMITAELFSQGPRPAAMSIAVLVNWIANFVVGLGFPTLN 477
           G + W++ +E+F    R  A++IAV   W+AN+ V   FP ++
Sbjct: 388 GPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMD 430



 Score = 33.5 bits (75), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 24/45 (53%)

Query: 1   MYISEIAPLNLRGGLGTVNQLAVTLGLLISQILGIEPILGTDEGW 45
           MYI+E+AP ++RG L + NQ A+  G L+   +        D  W
Sbjct: 149 MYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASW 193



 Score = 33.1 bits (74), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 29/58 (50%)

Query: 45  WPVLLDSRESDLHRSELENYTFLPFSVMLAVFWLFTYKKVPETKNKTFEEIVALFRTD 102
           W   +  + S L       +++  +  M  +  LF +K VPETK KT EE+ AL+  +
Sbjct: 424 WTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWEPE 481


  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    0.140    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,527,747
Number of Sequences: 62578
Number of extensions: 490495
Number of successful extensions: 893
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: 888
Number of HSP's gapped (non-prelim): 4
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
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: 53 (25.0 bits)