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= 021808
         (307 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 = 88.6 bits (218), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/298 (26%), Positives = 124/298 (41%), Gaps = 31/298 (10%)

Query: 1   MLGVSAVPAIIQFVLMLFMPESPRWLFMKSDKEKAILVLSKIYDIARLEDEIDHLSAAAE 60
           M     +PA++  +L+  +PESPRWL  +  +E+A  +L KI          + L+  A 
Sbjct: 202 MFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMG--------NTLATQAV 253

Query: 61  EELRK-----KKTVRYLDVFKSKEIRXXXXXXXXXXXXXXXXXINTVMYYSPTIVQMAGF 115
           +E++      +KT   L +F    I                  IN V+YY+P + +  G 
Sbjct: 254 QEIKHSLDHGRKTGGRLLMFGVGVI----VIGVMLSIFQQFVGINVVLYYAPEVFKTLG- 308

Query: 116 QSNQXXXXXXXXXXGTNAVGTIVGIYLIDHFGRKKLALSSLAGVIISLVLLSWAFIXXXX 175
            S              N   T++ I  +D FGRK L +    G+ I +  L  AF     
Sbjct: 309 ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAP 368

Query: 176 XXXXXVYGWIAVIGLALYIAFFAPGMGPVPWTLNSEVYPEQYRGICGGMSATVNWISNLI 235
                  G +A++ +  Y+A FA   GPV W L SE++P   RG    ++    W++N  
Sbjct: 369 -------GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYF 421

Query: 236 VAQTFLTVAE---LVG---TGATXXXXXXXXXXXXXXXXXXXPETQGLTFLEVEQMWK 287
           V+ TF  + +   LV     G +                   PET+G T  E+E +W+
Sbjct: 422 VSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479


  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
   0.321    0.136    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,940,507
Number of Sequences: 62578
Number of extensions: 215610
Number of successful extensions: 365
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 359
Number of HSP's gapped (non-prelim): 4
length of query: 307
length of database: 14,973,337
effective HSP length: 99
effective length of query: 208
effective length of database: 8,778,115
effective search space: 1825847920
effective search space used: 1825847920
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)