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= psy6665
         (420 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 = 90.9 bits (224), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 105/460 (22%), Positives = 185/460 (40%), Gaps = 81/460 (17%)

Query: 3   SRMNVYLATVLVGVVRMVFGLLTSQLLRTYGRRS-------LTMFSGLGMAVCMTTSGYY 55
           S +   +A+ L+G +  + G L       +GRR        L   SG+G A        +
Sbjct: 55  SLLGFCVASALIGCI--IGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSA--------W 104

Query: 56  TQLIMTGQIEKSLIPVFC------ILFYVAISVIAMGPSPAI--VYITEVARPDLRGALI 107
            +L  T     + +PV+        + Y  I  I +G +  +  +YI E+A   +RG L+
Sbjct: 105 PELGFTSINPDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLV 164

Query: 108 CIGPSITSLGMVIVYAL-------GAVLHWRTVAW--------------LSLAYILIPSP 146
                    G ++VY +       G      T  W              L L Y +  SP
Sbjct: 165 SFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESP 224

Query: 147 VWLLNKGRANQALKSLKYLARNYKEVKNKEQELKKMNSTKENQSLSARLIKMVTMATGIK 206
            WL+++G+  QA   L+ +  N    +   QE+K  +S    +    RL+       G+ 
Sbjct: 225 RWLMSRGKQEQAEGILRKIMGNTLATQ-AVQEIK--HSLDHGRKTGGRLLMF-----GVG 276

Query: 207 PLLVITVLFALQQLAGIYITIFYAVQFLEDMGSRMNV-YLATVLVGVVRMVFGLLTSQLL 265
            +++  +L   QQ  GI + ++YA +  + +G+  ++  L T++VGV+ + F +L    +
Sbjct: 277 VIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTV 336

Query: 266 RTYGRRSL----------------TMFSQIEKSLIPVFCILFYVAISVIGMLSIPWTMTA 309
             +GR+ L                T F      ++ +  +LFYVA   +    + W + +
Sbjct: 337 DKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLS 396

Query: 310 EIFPLEIRGIAQGLTFCLAHILMFFALQYYPWFKDSVGGSAMVQ-----WFFALXXXXXX 364
           EIFP  IRG A  +      +  +F    +P    +    A        W +        
Sbjct: 397 EIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAA 456

Query: 365 XXXXXFLPETHGRTLLEIEEYFETSCVYACSKKRRASAAI 404
                F+PET G+TL E+E  +E       +KK + +A +
Sbjct: 457 LFMWKFVPETKGKTLEELEALWEPE-----TKKTQQTATL 491


  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    0.139    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,987,307
Number of Sequences: 62578
Number of extensions: 350399
Number of successful extensions: 922
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 915
Number of HSP's gapped (non-prelim): 4
length of query: 420
length of database: 14,973,337
effective HSP length: 101
effective length of query: 319
effective length of database: 8,652,959
effective search space: 2760293921
effective search space used: 2760293921
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)