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= 008137
         (576 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 =  167 bits (422), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 118/366 (32%), Positives = 181/366 (49%), Gaps = 44/366 (12%)

Query: 19  NIVWTTPYIMKLALSAGIGGLLFGYDTGVISGAL-----LYIKEDFRDVEKKTWLQELIV 73
           N  + + YI  + L A +GGLLFGYDT VISG +     +++            L    V
Sbjct: 2   NTQYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCV 61

Query: 74  SMXXXXXXXXXXXXXWINDRFGRKISLLGADVLFFIGAI--------IMAIAPQPWV--- 122
           +              + ++RFGR+ SL  A VLFFI  +          +I P   V   
Sbjct: 62  ASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVY 121

Query: 123 -------IILGRIFVGLGVGMASMTAPLYISEASPAKIRGALVSANGFLITGGQFLAYLI 175
                   ++ RI  G+GVG+ASM +P+YI+E +PA IRG LVS N F I  GQ L Y +
Sbjct: 122 LAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCV 181

Query: 176 NLAFTKAPGT-------WRWMLGVAGLPAVVQFGLMMMLPESPRWLYRQNKVDEARAILE 228
           N    ++          WR+M     +PA++   L+  +PESPRWL  + K ++A  IL 
Sbjct: 182 NYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR 241

Query: 229 KIYPADQVEEEVNLLKQSVENEKAEEGLIGKDMISRLKGAFGNKIVRRGLYAGVTVQVAQ 288
           KI       + V  +K S+++ +   G        RL   FG  ++      GV + + Q
Sbjct: 242 KIMGNTLATQAVQEIKHSLDHGRKTGG--------RLL-MFGVGVI----VIGVMLSIFQ 288

Query: 289 QFVGINTVMYYSPTIVQFAGFASKSTALALSLVTSGLNALGSIVSMAFVDKYGRRRLMIV 348
           QFVGIN V+YY+P + +  G AS   AL  +++   +N   +++++  VDK+GR+ L I+
Sbjct: 289 QFVGINVVLYYAPEVFKTLG-ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQII 347

Query: 349 SMFGLS 354
              G++
Sbjct: 348 GALGMA 353



 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 9/122 (7%)

Query: 442 TYFISGCPSSFGWLAVVFLGAYIITYSPGMGTAPWIVNSEIYPLRYRGVGGGIAAVSNWT 501
           T F +  P     L+++F   Y+  ++   G   W++ SEI+P   RG    IA  + W 
Sbjct: 361 TAFYTQAPGIVALLSMLF---YVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWL 417

Query: 502 SNLIVSLTFLT------LTEALGSXXXXXXXXXXXXXXXXXIYLLVPETKGLAFEEVEKM 555
           +N  VS TF        L     +                 ++  VPETKG   EE+E +
Sbjct: 418 ANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEAL 477

Query: 556 LE 557
            E
Sbjct: 478 WE 479


>pdb|1NKW|F Chain F, Crystal Structure Of The Large Ribosomal Subunit From
           Deinococcus Radiodurans
 pdb|1NWX|F Chain F, Complex Of The Large Ribosomal Subunit From Deinococcus
           Radiodurans With Abt-773
 pdb|1NWY|F Chain F, Complex Of The Large Ribosomal Subunit From Deinococcus
           Radiodurans With Azithromycin
 pdb|1SM1|F Chain F, Complex Of The Large Ribosomal Subunit From Deinococcus
           Radiodurans With Quinupristin And Dalfopristin
 pdb|1XBP|F Chain F, Inhibition Of Peptide Bond Formation By Pleuromutilins:
           The Structure Of The 50s Ribosomal Subunit From
           Deinococcus Radiodurans In Complex With Tiamulin
          Length = 146

 Score = 29.3 bits (64), Expect = 6.5,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)

Query: 245 QSVENEKAEEGLIGKDMISRLKGAFGNKIVRRG---LYAGVTVQ 285
           +S+E  +A+E  + +D+ SRL G      VR G   +Y  VT Q
Sbjct: 51  RSIEKRQAQEKAVAEDLASRLNGVAVELSVRAGEGKIYGAVTHQ 94


>pdb|2WFL|A Chain A, Crystal Structure Of Polyneuridine Aldehyde Esterase
          Length = 264

 Score = 28.9 bits (63), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 112 IIMAIAPQPWVIILGRIFVGLGVGMASMTAPLYISEA 148
           ++ +I P   V++LG  F G+ +G+A  T P  IS A
Sbjct: 71  VMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVA 107


>pdb|2WFM|A Chain A, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Mutant (H244a)
 pdb|2WFM|B Chain B, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Mutant (H244a)
 pdb|2WFM|C Chain C, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Mutant (H244a)
 pdb|2WFM|D Chain D, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Mutant (H244a)
 pdb|2WFM|E Chain E, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Mutant (H244a)
          Length = 264

 Score = 28.9 bits (63), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 112 IIMAIAPQPWVIILGRIFVGLGVGMASMTAPLYISEA 148
           ++ +I P   V++LG  F G+ +G+A  T P  IS A
Sbjct: 71  VMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVA 107


>pdb|3GZJ|A Chain A, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Complexed With 16-Epi-Vellosimine
 pdb|3GZJ|B Chain B, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Complexed With 16-Epi-Vellosimine
 pdb|3GZJ|C Chain C, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Complexed With 16-Epi-Vellosimine
 pdb|3GZJ|D Chain D, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Complexed With 16-Epi-Vellosimine
 pdb|3GZJ|E Chain E, Crystal Structure Of Polyneuridine Aldehyde Esterase
           Complexed With 16-Epi-Vellosimine
          Length = 258

 Score = 28.9 bits (63), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 112 IIMAIAPQPWVIILGRIFVGLGVGMASMTAPLYISEA 148
           ++ +I P   V++LG  F G+ +G+A  T P  IS A
Sbjct: 65  VMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVA 101


>pdb|2WFL|B Chain B, Crystal Structure Of Polyneuridine Aldehyde Esterase
          Length = 264

 Score = 28.9 bits (63), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 112 IIMAIAPQPWVIILGRIFVGLGVGMASMTAPLYISEA 148
           ++ +I P   V++LG  F G+ +G+A  T P  IS A
Sbjct: 71  VMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVA 107


  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
   0.322    0.137    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,416,648
Number of Sequences: 62578
Number of extensions: 597278
Number of successful extensions: 1274
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1261
Number of HSP's gapped (non-prelim): 10
length of query: 576
length of database: 14,973,337
effective HSP length: 104
effective length of query: 472
effective length of database: 8,465,225
effective search space: 3995586200
effective search space used: 3995586200
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)