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= psy17080
         (565 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 = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 97/228 (42%), Gaps = 15/228 (6%)

Query: 257 YIAISGIAYY--SHNWRLLQWVITIPTIFFLTLWWIMPESPRWLVSMGRNKEAMKILGDA 314
           +IA SG A +  +  WR +     IP + FL L + +PESPRWL+S G+ ++A  IL   
Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGIL--- 240

Query: 315 AKFNSRXXXXXXXXXXXXSVLSTNQDVGKKVQVMDLWRTPLIRLISFVQYIIWFSXXXXX 374
            K                S L   +  G ++ +  +    +  ++S  Q  +  +     
Sbjct: 241 RKIMGNTLATQAVQEIKHS-LDHGRKTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYY 299

Query: 375 XXXXXNLSNIGGDV-YLNTIISGIVEFPAIVISIFILLKMGRRRPLCLTTLGAGLACLMT 433
                       D+  L TII G++     V++I  + K GR+    +  LG  +  + +
Sbjct: 300 APEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIG-MFS 358

Query: 434 LGF-----APGSFITIS-LAMVGKFAISSSNVIIPIYTAELFPTKMRN 475
           LG      APG    +S L  V  FA+S   V   +  +E+FP  +R 
Sbjct: 359 LGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCW-VLLSEIFPNAIRG 405


>pdb|1JP3|A Chain A, Structure Of E.Coli Undecaprenyl Pyrophosphate Synthase
 pdb|1JP3|B Chain B, Structure Of E.Coli Undecaprenyl Pyrophosphate Synthase
          Length = 253

 Score = 33.1 bits (74), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 23/98 (23%)

Query: 239 GKWLTIMGVMYLFPVPVG---------YIAISGI------AYYSHNW-RLLQWVITIPTI 282
           G+W    G +  F    G         + A +GI      A+ S NW R  Q V  +  +
Sbjct: 29  GRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALXEL 88

Query: 283 FFLTLWWIMPESPRWLVSMGRNKEAMKILGDAAKFNSR 320
           F   +W +  E    + S+ R+   ++I+GD ++FNSR
Sbjct: 89  F---VWALDSE----VKSLHRHNVRLRIIGDTSRFNSR 119


>pdb|1X08|A Chain A, Crystal Structure Of D26a Mutant Upps In Complex With Mg,
           Ipp And Fspp
 pdb|1X09|A Chain A, Crystal Structure Of The D26a Mutant Upps In Complex With
           Magnesium And Isopentenyl Pyrophosphate
          Length = 253

 Score = 32.3 bits (72), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 31/118 (26%), Positives = 51/118 (43%), Gaps = 31/118 (26%)

Query: 219 GFFCVSIVFSGFVLCMELVGGKWLTIMGVMYLFPVPVG---------YIAISGI------ 263
           G   V+I+ +G         G+W    G +  F    G         + A +GI      
Sbjct: 17  GCRHVAIIMAG--------NGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLY 68

Query: 264 AYYSHNW-RLLQWVITIPTIFFLTLWWIMPESPRWLVSMGRNKEAMKILGDAAKFNSR 320
           A+ S NW R  Q V  +  +F   +W +  E    + S+ R+   ++I+GD ++FNSR
Sbjct: 69  AFSSENWNRPAQEVSALMELF---VWALDSE----VKSLHRHNVRLRIIGDTSRFNSR 119


>pdb|1UEH|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Triton X- 100, Magnesium And Sulfate
 pdb|1UEH|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Triton X- 100, Magnesium And Sulfate
 pdb|1V7U|A Chain A, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
           With Farnesyl Pyrophosphate
 pdb|1V7U|B Chain B, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
           With Farnesyl Pyrophosphate
 pdb|1X06|A Chain A, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
           In Complex With Mg, Ipp And Fspp
 pdb|1X07|A Chain A, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
           In Complex With Mg And Ipp
 pdb|2E98|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-629
 pdb|2E98|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-629
 pdb|2E99|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-608
 pdb|2E99|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-608
 pdb|2E9A|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-628
 pdb|2E9A|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-628
 pdb|2E9C|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-675
 pdb|2E9C|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-675
 pdb|2E9D|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-676
 pdb|2E9D|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
           With Bph-676
 pdb|3QAS|B Chain B, Structure Of Undecaprenyl Diphosphate Synthase
 pdb|3QAS|A Chain A, Structure Of Undecaprenyl Diphosphate Synthase
 pdb|3TH8|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase
           Complexed With Bph-1063
 pdb|3TH8|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase
           Complexed With Bph-1063
 pdb|3SGT|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1299
 pdb|3SGT|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1299
 pdb|3SGV|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1290
 pdb|3SGV|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1290
 pdb|3SGX|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1100
 pdb|3SGX|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1100
 pdb|3SH0|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1065
 pdb|3SH0|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
           Synthase In Complex With Bph-1065
 pdb|4H2J|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1354
 pdb|4H2J|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1354
 pdb|4H2M|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1408
 pdb|4H2M|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1408
 pdb|4H2O|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1248
 pdb|4H2O|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1248
 pdb|4H38|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1297
 pdb|4H38|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1297
 pdb|4H3A|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1330
 pdb|4H3A|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-1330
 pdb|4H3C|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-987
 pdb|4H3C|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
           Complex With Bph-987
          Length = 253

 Score = 32.3 bits (72), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 23/98 (23%)

Query: 239 GKWLTIMGVMYLFPVPVG---------YIAISGI------AYYSHNW-RLLQWVITIPTI 282
           G+W    G +  F    G         + A +GI      A+ S NW R  Q V  +  +
Sbjct: 29  GRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMEL 88

Query: 283 FFLTLWWIMPESPRWLVSMGRNKEAMKILGDAAKFNSR 320
           F   +W +  E    + S+ R+   ++I+GD ++FNSR
Sbjct: 89  F---VWALDSE----VKSLHRHNVRLRIIGDTSRFNSR 119


  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
   0.326    0.140    0.446 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,709,745
Number of Sequences: 62578
Number of extensions: 536095
Number of successful extensions: 1229
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1226
Number of HSP's gapped (non-prelim): 6
length of query: 565
length of database: 14,973,337
effective HSP length: 104
effective length of query: 461
effective length of database: 8,465,225
effective search space: 3902468725
effective search space used: 3902468725
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)