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= 043264
         (435 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 = 96.7 bits (239), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 79/302 (26%), Positives = 137/302 (45%), Gaps = 28/302 (9%)

Query: 139 RVFTGLGIGFINQTAPIYLVEMAPTKWRGAIGTGFQIFFWSGVAGASWINYFIMSS---- 194
           R+  G+G+G  +  +P+Y+ E+AP   RG + +  Q     G      +NYFI  S    
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192

Query: 195 -LNFKRWRIAVSVSGFPATLMTIIAFFIPDTPSSLIQRGKVQQALKSLNQVRGTKFDSE- 252
            LN   WR   +    PA L  ++ + +P++P  L+ RGK +QA   L ++ G    ++ 
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQA 252

Query: 253 -NELKYLIKYNEDMRIASETPYKMLLERKYRPHLLFAIALPTFQALTGFNLNAVVGQLIV 311
             E+K+ + +        +T  ++L+       ++  + L  FQ   G N+       + 
Sbjct: 253 VQEIKHSLDHGR------KTGGRLLMFGV--GVIVIGVMLSIFQQFVGINVVLYYAPEVF 304

Query: 312 TSLGIRLKDVFPILIIQSTIFFVCLLLTGYLIDRVGRRIMLIVGGCQIFICQVILAILMA 371
            +LG          II   I     +L    +D+ GR+ + I+G           A+ MA
Sbjct: 305 KTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIG-----------ALGMA 353

Query: 372 SESRSHGTSIFSKRSAFVALILRCFLGVGMALSWGPLPWILNCEILPIEVRSAGQGLSTA 431
               S GT+ +++    VAL+   F     A+SWGP+ W+L  EI P  +R  G+ L+ A
Sbjct: 354 IGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIR--GKALAIA 411

Query: 432 IS 433
           ++
Sbjct: 412 VA 413


  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    0.142    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,133,378
Number of Sequences: 62578
Number of extensions: 419896
Number of successful extensions: 838
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 832
Number of HSP's gapped (non-prelim): 4
length of query: 435
length of database: 14,973,337
effective HSP length: 102
effective length of query: 333
effective length of database: 8,590,381
effective search space: 2860596873
effective search space used: 2860596873
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: 53 (25.0 bits)