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= 018373
         (357 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 = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 61/255 (23%), Positives = 100/255 (39%), Gaps = 49/255 (19%)

Query: 48  NWRWLLAFSSVPSFALLLFYGLAPESPRYLCAKARTVDAHRILEKMAFVNQTKLPPGILV 107
            WR++ A   +P+   L+     PESPR+L ++ +   A  IL K+          G  +
Sbjct: 198 GWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIM---------GNTL 248

Query: 108 SDKAIKENEESNLLRDTHMLSMTRKITDKLKSGFSSFFMLFSRKLIRTTLLLWVL--FFA 165
           + +A++E +        H L   RK   +L        ++F   +I   ++L +   F  
Sbjct: 249 ATQAVQEIK--------HSLDHGRKTGGRL--------LMFGVGVIVIGVMLSIFQQFVG 292

Query: 166 -NVFSYYGAVLLTSKLSSGDNKCGSKVLHADKSKDNSLYVDVFIASLAELPGLILSAIIV 224
            NV  YY   +              K L A  S D +L +   I  +  L   +L+ + V
Sbjct: 293 INVVLYYAPEVF-------------KTLGA--STDIAL-LQTIIVGVINLTFTVLAIMTV 336

Query: 225 DKIGRKLSMVLMFVSACI--FLLPLVFHQSA---VVTTVLLFGVRMCVTGTITVATIYAP 279
           DK GRK   ++  +   I  F L   F+  A   V    +LF V         V  +   
Sbjct: 337 DKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLS 396

Query: 280 EIYPTSARTTGFGVA 294
           EI+P + R     +A
Sbjct: 397 EIFPNAIRGKALAIA 411


>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 35.0 bits (79), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 45/204 (22%), Positives = 79/204 (38%), Gaps = 26/204 (12%)

Query: 115 NEESNLLRDTHMLSMTRKITDKLKSGFSSFFMLFSRKLIRTTLLLWVLFFANVFSYYGAV 174
            E  N   D +     +++T K        FM    + +    LLW +  ANVF Y    
Sbjct: 220 EEYKNDYPDDYNEKAEQELTAK------QIFM----QYVLPNKLLWYIAIANVFVY---- 265

Query: 175 LLTSKLSSGDNKCGSKVLHADKSKDNSLYVDVFIASLAELPGLILSAIIVDKIGRK---- 230
           LL   +         +V H    K +  Y   F+   A +PG +L   + DK+ R     
Sbjct: 266 LLRYGILDWSPTYLKEVKHFALDKSSWAY---FLYEYAGIPGTLLCGWMSDKVFRGNRGA 322

Query: 231 ---LSMVLMFVSACIFLLPLVFHQSAVVTTVLLFGVRMCVTGTITVATIYAPEIYPTSAR 287
                M L+ ++  ++ +    + +  +  +++ G    + G + +  ++A E+ P  A 
Sbjct: 323 TGVFFMTLVTIATIVYWMNPAGNPTVDMICMIVIG--FLIYGPVMLIGLHALELAPKKAA 380

Query: 288 TTGFGVASSLGKVGGMVCPLVAVG 311
            T  G     G +GG V     VG
Sbjct: 381 GTAAGFTGLFGYLGGSVAASAIVG 404


  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
   0.327    0.138    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,208,709
Number of Sequences: 62578
Number of extensions: 329942
Number of successful extensions: 655
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 651
Number of HSP's gapped (non-prelim): 5
length of query: 357
length of database: 14,973,337
effective HSP length: 100
effective length of query: 257
effective length of database: 8,715,537
effective search space: 2239893009
effective search space used: 2239893009
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)