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= 035636
         (515 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 =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 140/498 (28%), Positives = 234/498 (46%), Gaps = 60/498 (12%)

Query: 22  YVVACVIIAAFGGLMFGYDIG-ISGGVTAMDDFLERFFPRVYEKKKHAHEDNYCKYDNQF 80
           Y+ +  ++A  GGL+FGYD   ISG V +++         V+   ++  E       N  
Sbjct: 9   YIFSITLVATLGGLLFGYDTAVISGTVESLNT--------VFVAPQNLSESA----ANSL 56

Query: 81  LQLFTSCLYLAALIASFVASRVCSKQGRRPTMQIAS-FFFLVGV---------------- 123
           L    +   +  +I   +     ++ GRR +++IA+  FF+ GV                
Sbjct: 57  LGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDN 116

Query: 124 -VLTSAAFHISMLILGRLALGIGVGFANQAVPLFLSELAPAKIRGALNISFQLF-ITIGI 181
            V    A ++   ++ R+  GIGVG A+   P++++ELAPA IRG L +SF  F I  G 
Sbjct: 117 TVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKL-VSFNQFAIIFGQ 175

Query: 182 FIANMVNYAMSN------VHPYGWRLSLAIAGVPALFLCVGSMSICETPTSLIERGRLEE 235
            +   VNY ++       ++  GWR   A   +PAL   +   ++ E+P  L+ RG+ E+
Sbjct: 176 LLVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQ 235

Query: 236 GRVVLQRIRGVANVDNEFDSIVHACEMANQVTKPFSKLMKRSSRPPLVIAILLQVFQQFT 295
              +L++I G          I H+ +      K   +L+       +VI ++L +FQQF 
Sbjct: 236 AEGILRKIMGNTLATQAVQEIKHSLDHGR---KTGGRLLMFGVGV-IVIGVMLSIFQQFV 291

Query: 296 GINAIMFYAPVLFQTVGFGSEASLLSAVITGLVNVFSTLVSVYAVDKAGRRALLLEAVVQ 355
           GIN +++YAP +F+T+G  ++ +LL  +I G++N+  T++++  VDK GR+ L +   + 
Sbjct: 292 GINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALG 351

Query: 356 MFITQSIIGIILAIWLKPTGSLNKXXXXXXXXXXXXXXMGFAWSWGPLGWLIPSETFPLE 415
           M I    +G         T    +                FA SWGP+ W++ SE FP  
Sbjct: 352 MAIGMFSLG---------TAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNA 402

Query: 416 TRTAGFAFAVSTNMLFTFLVAQAFLSMLCN--MKAGIFFFFAAWI-----VVMGLFAMFL 468
            R    A AV+   L  + V+  F  M  N  + A     F+ WI     V+  LF    
Sbjct: 403 IRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKF 462

Query: 469 LPETKGVPVDAVTERVWK 486
           +PETKG  ++ + E +W+
Sbjct: 463 VPETKGKTLEEL-EALWE 479


>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation.
 pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
           An Inward Open Conformation
          Length = 491

 Score = 33.9 bits (76), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 56/131 (42%), Gaps = 7/131 (5%)

Query: 81  LQLFTSCLYLAALIASFVASRVCSKQGRRPTMQIASFFFLVGVVLTSAAFHISMLILGRL 140
           + ++ S +YL+  I  FVA R+    G RP +       ++G ++ +  F  S L    +
Sbjct: 60  MAIYASMVYLSGTIGGFVADRII---GARPAVFWGGVLIMLGHIVLALPFGASALFGSII 116

Query: 141 ALGIGVGFANQAVPLFLSELAPAKIRGALNISFQLF---ITIGIFIANMVNYAMSNVHPY 197
            + IG GF    V   +  L     R   +  F +F   I +G FIA ++  A      Y
Sbjct: 117 LIIIGTGFLKPNVSTLVGTLYDEHDR-RRDAGFSIFVFGINLGAFIAPLIVGAAQEAAGY 175

Query: 198 GWRLSLAIAGV 208
               SLA  G+
Sbjct: 176 HVAFSLAAIGM 186


  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
   0.329    0.141    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,577,772
Number of Sequences: 62578
Number of extensions: 510560
Number of successful extensions: 1437
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: 1428
Number of HSP's gapped (non-prelim): 4
length of query: 515
length of database: 14,973,337
effective HSP length: 103
effective length of query: 412
effective length of database: 8,527,803
effective search space: 3513454836
effective search space used: 3513454836
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: 54 (25.4 bits)