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= 009362
         (536 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 = 29.3 bits (64), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 61/307 (19%), Positives = 113/307 (36%), Gaps = 41/307 (13%)

Query: 205 AWRLILMLGSIPAAFTYYWRMTMPESARYTALVEQNVMQAAKDMEKVLDVSI-SQIAEEX 263
            WR +     IPA        T+PES R+  +      QA   + K++  ++ +Q  +E 
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWL-MSRGKQEQAEGILRKIMGNTLATQAVQEI 256

Query: 264 XXXXXXXXXXXISKRFLRRHGRDLFACATSWLLVDIVFYSSNLFQSKIYHQYIDGNGHDQ 323
                       S    R+ G  L       +++ ++          I+ Q++   G + 
Sbjct: 257 KH----------SLDHGRKTGGRLLMFGVGVIVIGVML--------SIFQQFV---GINV 295

Query: 324 TRSAFEEAFKVARHQAIFAICSTIPGYFVTVFF-------IDRIGRVAIQALGFFFMGVI 376
                 E FK        A+  TI    + + F       +D+ GR  +Q +G   M + 
Sbjct: 296 VLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIG 355

Query: 377 YLAIGVPYSYKWSKHTNFGFMFLYALTFFFANF----GPNTTTFIVPAELFPARFRSTCH 432
             ++G  +  +       G + L ++ F+ A F    GP    +++ +E+FP   R    
Sbjct: 356 MFSLGTAFYTQAP-----GIVALLSMLFYVAAFAMSWGP--VCWVLLSEIFPNAIRGKAL 408

Query: 433 GISGAFGKVGAIIGTVAFLWASHDDNKVNATGVTIALLILGGVCFMGFAITYFFTRETMG 492
            I+ A   +     +  F     +   V       +  I G +  +     + F  ET G
Sbjct: 409 AIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKG 468

Query: 493 RSLEENE 499
           ++LEE E
Sbjct: 469 KTLEELE 475


  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
   0.328    0.139    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,443,483
Number of Sequences: 62578
Number of extensions: 497467
Number of successful extensions: 1151
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1147
Number of HSP's gapped (non-prelim): 7
length of query: 536
length of database: 14,973,337
effective HSP length: 103
effective length of query: 433
effective length of database: 8,527,803
effective search space: 3692538699
effective search space used: 3692538699
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)