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= 008624
         (559 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 =  115 bits (287), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 91/304 (29%), Positives = 147/304 (48%), Gaps = 33/304 (10%)

Query: 217 APLYIAETCPSQIRGTLISLKELFIVLGILLGYFVGSFQINA-------VGGWRYMYGLS 269
           +P+YIAE  P+ IRG L+S  +  I+ G LL Y V  F   +         GWRYM+   
Sbjct: 147 SPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASE 206

Query: 270 APLALLMGIGMXXXXXXXXXXXXXAVQGKGSLQEYKEQAISALGKLRRRPPGDKLSERQI 329
              ALL    +               +GK      +EQA   L    R+  G+ L+ + +
Sbjct: 207 CIPALLF---LMLLYTVPESPRWLMSRGK------QEQAEGIL----RKIMGNTLATQAV 253

Query: 330 EDTLVSLKSSYTDEKSEGSFLEVFQGPNLKAFIIGGGLVLFQQITGQPSVLYYAGPILQS 389
           ++    +K S    +  G  L +F    +   +IG  L +FQQ  G   VLYYA  + ++
Sbjct: 254 QE----IKHSLDHGRKTGGRLLMF---GVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKT 306

Query: 390 AGFSAAAD-ATRVSVVIGVFKLVMTWIAVAKVDDLGRRPL-LIGGVCXXXXXXXXXXXXX 447
            G  A+ D A   ++++GV  L  T +A+  VD  GR+PL +IG +              
Sbjct: 307 LG--ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFY 364

Query: 448 XXXXGFPLVAVSALLLYVGCYQISFGPISWLMVSEIFPLRTRGRGISLAVLTNFGSNAIV 507
               G  +VA+ ++L YV  + +S+GP+ W+++SEIFP   RG+ +++AV   + +N  V
Sbjct: 365 TQAPG--IVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFV 422

Query: 508 TFAF 511
           ++ F
Sbjct: 423 SWTF 426


  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    0.138    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,220,314
Number of Sequences: 62578
Number of extensions: 449630
Number of successful extensions: 812
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: 807
Number of HSP's gapped (non-prelim): 1
length of query: 559
length of database: 14,973,337
effective HSP length: 104
effective length of query: 455
effective length of database: 8,465,225
effective search space: 3851677375
effective search space used: 3851677375
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: 54 (25.4 bits)