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= 010317
         (513 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 =  158 bits (400), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 140/528 (26%), Positives = 219/528 (41%), Gaps = 88/528 (16%)

Query: 27  NKYAFICALLASINSILLGYDIGVMSGAVLYIKEDL----EITEVQVEVLVGILNVFSLI 82
           + Y F   L+A++  +L GYD  V+SG V  +         ++E     L+G     +LI
Sbjct: 7   SSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALI 66

Query: 83  GSLASGK----TSDYIGRRYTIVVAAATFLVGALAMG------------------LAPNY 120
           G +  G      S+  GRR ++ +AA  F +  +                     LA   
Sbjct: 67  GCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYV 126

Query: 121 PFLIVGRMIAGIGVGYSLMISPVYTAEISPTMKRGFLTSLPEVFIVLGILSGYVFNY--A 178
           P  ++ R+I GIGVG + M+SP+Y AE++P   RG L S  +  I+ G L  Y  NY  A
Sbjct: 127 PEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIA 186

Query: 179 LSGLPGNIN---WRIMXXXXXXXXXXXXXXXXXMPESPRWLVMKSRYDEAKRVLLKV--- 232
            SG    +N   WR M                 +PESPRWL+ + + ++A+ +L K+   
Sbjct: 187 RSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246

Query: 233 ---SDTEQEAKERLDDMIKAAKEXXXXXXXXXXXXXXXNFTGEGVWKDLILKPTPAVRRM 289
              +   QE K  LD   K                      G GV               
Sbjct: 247 TLATQAVQEIKHSLDHGRKTGGRLLMF--------------GVGV--------------- 277

Query: 290 LIAAVGINFFMQASGNDAVIYYTPAVFKGAGIHRKPVLFGINVVMGLAKTFFVVLSALHL 349
           ++  V ++ F Q  G + V+YY P VFK  G      L    +++G+    F VL+ + +
Sbjct: 278 IVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQ-TIIVGVINLTFTVLAIMTV 336

Query: 350 DKFGRRPXXXXXXXXXXXXXXXXXXXXXXXXXXTPTXXXXXXXXXXXXXXSFFSIGLGPI 409
           DKFGR+P                                           + F++  GP+
Sbjct: 337 DKFGRKPLQIIGALGMAIGMFSLGTAFYT------QAPGIVALLSMLFYVAAFAMSWGPV 390

Query: 410 TWVYSSEIFPLRLRAQGSALAISVNRLVSGVISMTF-------LSISHRLSFGGTFFLLA 462
            WV  SEIFP  +R +  A+A++   L +  +S TF         ++H    G ++++  
Sbjct: 391 CWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAH-FHNGFSYWIYG 449

Query: 463 GITTVGTIFFYVFLPETKGKTLEEMQALFGGDNDDTSRDENEKQQTET 510
            +  +  +F + F+PETKGKTLEE++AL+  +   T       QQT T
Sbjct: 450 CMGVLAALFMWKFVPETKGKTLEELEALWEPETKKT-------QQTAT 490


>pdb|2GFP|A Chain A, Structure Of The Multidrug Transporter Emrd From
           Escherichia Coli
 pdb|2GFP|B Chain B, Structure Of The Multidrug Transporter Emrd From
           Escherichia Coli
          Length = 375

 Score = 28.9 bits (63), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 30/59 (50%)

Query: 54  AVLYIKEDLEITEVQVEVLVGILNVFSLIGSLASGKTSDYIGRRYTIVVAAATFLVGAL 112
           A+  +  DL + E  V+ ++G   +   +  L  G  SD +GRR  I+V  + F++  L
Sbjct: 22  AIADMARDLNVREGAVQSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATL 80


  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    0.139    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,631,687
Number of Sequences: 62578
Number of extensions: 458726
Number of successful extensions: 905
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 896
Number of HSP's gapped (non-prelim): 8
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
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)