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= 016515
         (388 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 = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 72/307 (23%), Positives = 117/307 (38%), Gaps = 65/307 (21%)

Query: 39  YFLEFVPVSHRGRWMVALSAFWTAGTIFEASLAWVV------------MTRLNWRWLLAF 86
           Y  E  P   RG+ +V+ + F     IF   L + V            +    WR++ A 
Sbjct: 150 YIAELAPAHIRGK-LVSFNQF---AIIFGQLLVYCVNYFIARSGDASWLNTDGWRYMFAS 205

Query: 87  SSVPSFALLLFYGLAPESPRYLCAKARTVDAHRILEKMAFVNQTKLPPGILVSDKAIKEN 146
             +P+   L+     PESPR+L ++ +   A  IL K+          G  ++ +A++E 
Sbjct: 206 ECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIM---------GNTLATQAVQEI 256

Query: 147 EESNLLRDTHMLSMTRKITDKLKSGFSSFFMLFSRKLIRTTLLLWVL--FFA-NVFSYYG 203
           +        H L   RK   +L        ++F   +I   ++L +   F   NV  YY 
Sbjct: 257 K--------HSLDHGRKTGGRL--------LMFGVGVIVIGVMLSIFQQFVGINVVLYYA 300

Query: 204 AVLLTSKLSSGDNKCGSKVLHADKSKDNSLYVDVFIASLAELPGLILSAIIVDKIGRKLS 263
             +              K L A  S D +L +   I  +  L   +L+ + VDK GRK  
Sbjct: 301 PEVF-------------KTLGA--STDIAL-LQTIIVGVINLTFTVLAIMTVDKFGRKPL 344

Query: 264 MVLMFVSACI--FLLPLVFHQSA---VVTTVLLFGVRMCVTGTITVATIYAPEIYPTSAR 318
            ++  +   I  F L   F+  A   V    +LF V         V  +   EI+P + R
Sbjct: 345 QIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIR 404

Query: 319 TTGFGVA 325
                +A
Sbjct: 405 GKALAIA 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 = 0.070,   Method: Compositional matrix adjust.
 Identities = 45/204 (22%), Positives = 79/204 (38%), Gaps = 26/204 (12%)

Query: 146 NEESNLLRDTHMLSMTRKITDKLKSGFSSFFMLFSRKLIRTTLLLWVLFFANVFSYYGAV 205
            E  N   D +     +++T K        FM    + +    LLW +  ANVF Y    
Sbjct: 220 EEYKNDYPDDYNEKAEQELTAK------QIFM----QYVLPNKLLWYIAIANVFVY---- 265

Query: 206 LLTSKLSSGDNKCGSKVLHADKSKDNSLYVDVFIASLAELPGLILSAIIVDKIGRK---- 261
           LL   +         +V H    K +  Y   F+   A +PG +L   + DK+ R     
Sbjct: 266 LLRYGILDWSPTYLKEVKHFALDKSSWAY---FLYEYAGIPGTLLCGWMSDKVFRGNRGA 322

Query: 262 ---LSMVLMFVSACIFLLPLVFHQSAVVTTVLLFGVRMCVTGTITVATIYAPEIYPTSAR 318
                M L+ ++  ++ +    + +  +  +++ G    + G + +  ++A E+ P  A 
Sbjct: 323 TGVFFMTLVTIATIVYWMNPAGNPTVDMICMIVIG--FLIYGPVMLIGLHALELAPKKAA 380

Query: 319 TTGFGVASSLGKVGGMVCPLVAVG 342
            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    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,500,173
Number of Sequences: 62578
Number of extensions: 334529
Number of successful extensions: 662
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: 658
Number of HSP's gapped (non-prelim): 5
length of query: 388
length of database: 14,973,337
effective HSP length: 101
effective length of query: 287
effective length of database: 8,652,959
effective search space: 2483399233
effective search space used: 2483399233
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)