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= 005249
         (706 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 =  107 bits (266), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 35/236 (14%)

Query: 7   VAIAATIGNFLQGWDNATIAGAI-----VYIKKDLNL----GTTVEGLVVAMSLIGATAI 57
           + + AT+G  L G+D A I+G +     V++    NL      ++ G  VA +LIG    
Sbjct: 13  ITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQ-NLSESAANSLLGFCVASALIGCIIG 71

Query: 58  TTCSGPISDWLGRRPMLILSSVLYFVSGLVMLW--------SPN----VYV------LCI 99
               G  S+  GRR  L +++VL+F+SG+   W        +P+    VY+        I
Sbjct: 72  GALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVI 131

Query: 100 ARLLDGFGVGLAVTLVPLYISETAPSEIRGRLNTLPQFTGSGGMFLAYCMVFGM------ 153
            R++ G GVGLA  L P+YI+E AP+ IRG+L +  QF    G  L YC+ + +      
Sbjct: 132 YRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDA 191

Query: 154 SLLASPSWRLMLGVLSIPXXXXXXXXXXXXPESPRWLVSKGKMLEAKQVLQRLRGR 209
           S L +  WR M     IP            PESPRWL+S+GK  +A+ +L+++ G 
Sbjct: 192 SWLNTDGWRYMFASECIP-ALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246



 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/261 (25%), Positives = 111/261 (42%), Gaps = 35/261 (13%)

Query: 458 YDVPEEGEYIQAAALVSQPALYSKELMDQHPVGPAMVHPSETASKG-PSWAALLEAGVKR 516
           Y VPE   ++ +     Q     +++M       A+     +   G  +   LL  GV  
Sbjct: 218 YTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVG- 276

Query: 517 ALLVGVGIQILQQFSGINGVLYYTPQILEQAG----------------------VAMKLM 554
            +++GV + I QQF GIN VLYY P++ +  G                      +A+  +
Sbjct: 277 VIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTV 336

Query: 555 DVAGRRKXXXXXXXXXXXXXXXXXXXXXXQLISPVLKAGISTACVIIYFCCFVAAYGPIP 614
           D  GR+                       Q  +P + A +S   ++ Y   F  ++GP+ 
Sbjct: 337 DKFGRKPLQIIGALGMAIGMFSLGTAFYTQ--APGIVALLS---MLFYVAAFAMSWGPVC 391

Query: 615 NILCAEIFPTKVRGICIAICAMAYWICDIIVTYTLPVMLSSIGLAGAFG------VYAVV 668
            +L +EIFP  +RG  +AI   A W+ +  V++T P+M  +  L   F       +Y  +
Sbjct: 392 WVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCM 451

Query: 669 CFISWVFVFLRVPETKGMPLE 689
             ++ +F++  VPETKG  LE
Sbjct: 452 GVLAALFMWKFVPETKGKTLE 472


>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 = 30.4 bits (67), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 10/78 (12%)

Query: 28  AIVYIKKDLNLGTTVEGLVVAMSLIGATAIT-----TCSGPISDWLGRRPMLILSSVLYF 82
           AI  + +DLN+    EG V   S++GA  +T        GPISD +GRRP++++   ++ 
Sbjct: 22  AIADMARDLNVR---EGAV--QSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFM 76

Query: 83  VSGLVMLWSPNVYVLCIA 100
           ++ LV + + ++ VL  A
Sbjct: 77  LATLVAVTTSSLTVLIAA 94


  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
   0.320    0.137    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,608,871
Number of Sequences: 62578
Number of extensions: 782059
Number of successful extensions: 1632
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: 1621
Number of HSP's gapped (non-prelim): 8
length of query: 706
length of database: 14,973,337
effective HSP length: 106
effective length of query: 600
effective length of database: 8,340,069
effective search space: 5004041400
effective search space used: 5004041400
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)