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= psy16653
         (301 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 = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 53/98 (54%), Gaps = 6/98 (6%)

Query: 110 PETPIYLMKSGNNKKAEVSLRFYRGSRYDVPLELAAIQREIDAAARKKASFSDLVSSRAN 169
           PE+P +LM  G  ++AE  LR   G+     L   A+Q    +    + +   L+     
Sbjct: 221 PESPRWLMSRGKQEQAEGILRKIMGNT----LATQAVQEIKHSLDHGRKTGGRLL--MFG 274

Query: 170 LRALIISLGLMVFQQFSGVNAVIFYSNDIFKSAGSTLD 207
           +  ++I + L +FQQF G+N V++Y+ ++FK+ G++ D
Sbjct: 275 VGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTD 312



 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 222 DCIPFQVKGIATGIAVAVNWIGAFLVTLCF------GFLVRHFGSAATFWIXXXXXXXXX 275
           +  P  ++G A  IAVA  W+  + V+  F       +LV HF +  ++WI         
Sbjct: 397 EIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAA 456

Query: 276 XXXXXXXPETKGKTLAQIQ 294
                  PETKGKTL +++
Sbjct: 457 LFMWKFVPETKGKTLEELE 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
   0.323    0.139    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,327,619
Number of Sequences: 62578
Number of extensions: 251992
Number of successful extensions: 422
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: 418
Number of HSP's gapped (non-prelim): 2
length of query: 301
length of database: 14,973,337
effective HSP length: 98
effective length of query: 203
effective length of database: 8,840,693
effective search space: 1794660679
effective search space used: 1794660679
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)