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= psy3965
         (535 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 = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/239 (23%), Positives = 104/239 (43%), Gaps = 37/239 (15%)

Query: 275 SWRILQWVITAPTIIFLILWWCIPESPRWLLTMGKTEEAMEVLKDAARFNDKTLPANTDK 334
            WR +      P ++FL+L + +PESPRWL++ GK E+A  +L+   +    TL     +
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR---KIMGNTLATQAVQ 254

Query: 335 LLKQSVSSMKEDSGKKVEVLDLWRTPLMRLISCVQYVVWFSXXXXXXXXXXNLSNIGGDV 394
            +K S+   ++ +G ++ +  +    +  ++S  Q  V                     +
Sbjct: 255 EIKHSLDHGRK-TGGRLLMFGVGVIVIGVMLSIFQQFV--------------------GI 293

Query: 395 YVNTVISGESFNSTTLSTSSILCFHDLSTSCVPGIVEIPAIAMSILILLKMGRRRPLCLT 454
            V    + E F +   ST   L       + + G++ +    ++I+ + K G R+PL + 
Sbjct: 294 NVVLYYAPEVFKTLGASTDIALL-----QTIIVGVINLTFTVLAIMTVDKFG-RKPLQII 347

Query: 455 ---TMAAGVACLVTLAFPQGSWMTISLAM---IGKFAISSSNVVMPVYTAELFPTKMRN 507
               MA G+  L T  + Q   +   L+M   +  FA+S   V   V  +E+FP  +R 
Sbjct: 348 GALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCW-VLLSEIFPNAIRG 405


  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    0.135    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,038,261
Number of Sequences: 62578
Number of extensions: 599897
Number of successful extensions: 1090
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1088
Number of HSP's gapped (non-prelim): 5
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
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: 54 (25.4 bits)