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= 048448
         (308 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 = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/138 (30%), Positives = 64/138 (46%), Gaps = 23/138 (16%)

Query: 86  VARKGAAPLLDFGRFLAGCGIGVMSYVVPVYIAEITPKNLRAALATVNQLFIVTGALFAY 145
           V   G  P     R + G G+G+ S + P+YIAE+ P ++R  L + NQ  I+ G L  Y
Sbjct: 120 VYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVY 179

Query: 146 VIGALMS------------WR----------ILALTGLFFIPESPRWLAMIGKNQEFEVA 183
            +   ++            WR          +L L  L+ +PESPRWL   GK ++ E  
Sbjct: 180 CVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGI 239

Query: 184 LSMVRGPNVDVSRELNEI 201
           L  + G N   ++ + EI
Sbjct: 240 LRKIMG-NTLATQAVQEI 256



 Score = 39.7 bits (91), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 31/48 (64%)

Query: 240 YIAFYSIGMGPIPWVIMFEIFPLNIKGPGGSLVTLVNWIGSWAISYSF 287
           Y+A +++  GP+ WV++ EIFP  I+G   ++     W+ ++ +S++F
Sbjct: 379 YVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTF 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
   0.322    0.138    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,226,814
Number of Sequences: 62578
Number of extensions: 300487
Number of successful extensions: 736
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 732
Number of HSP's gapped (non-prelim): 34
length of query: 308
length of database: 14,973,337
effective HSP length: 99
effective length of query: 209
effective length of database: 8,778,115
effective search space: 1834626035
effective search space used: 1834626035
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)