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= 042942
         (189 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 = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 76  RVLLGVGIGFANQSVPLYLSEMAPPKNRGAFNIGFQVSVGIGVLSDNLLNYGTEKI-NGG 134
           R++ G+G+G A+   P+Y++E+AP   RG      Q ++  G L    +NY   +  +  
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192

Query: 135 W----GWRISLAMAAAPASILTIETKNLP 159
           W    GWR   A    PA +  +    +P
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVP 221


>pdb|3BE5|A Chain A, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE5|B Chain B, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE5|C Chain C, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE5|D Chain D, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE6|A Chain A, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE6|B Chain B, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE6|C Chain C, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
           Periplasmic Siderophore Binding Protein
 pdb|3BE6|D Chain D, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
           Periplasmic Siderophore Binding Protein
          Length = 297

 Score = 27.7 bits (60), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 139 ISLAMAAAPASILTIETKNLPIEQMDKL 166
           I   +AA P  I+T  T+N PIE+++K+
Sbjct: 83  IEAIVAAKPDLIITEPTRNTPIERLEKI 110


>pdb|3VMN|A Chain A, Crystal Structure Of Dextranase From Streptococcus Mutans
 pdb|3VMO|A Chain A, Crystal Structure Of Dextranase From Streptococcus Mutans
           In Complex With Isomaltotriose
 pdb|3VMP|A Chain A, Crystal Structure Of Dextranase From Streptococcus Mutans
           In Complex With 4,5-Epoxypentyl Alpha-D-Glucopyranoside
          Length = 643

 Score = 27.7 bits (60), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 36/90 (40%), Gaps = 8/90 (8%)

Query: 85  FANQSVPLYLSEMAPPKNRGAFNIGFQVSVGIGVLSDNLLNYGTEKINGGWGWRISLAMA 144
             N+S      E   P N  A N G+ + V I    +N+L  G   I     WR     A
Sbjct: 63  LPNESYTTQKGEFVIPANSLANNRGYLLKVNISDSQNNILEQGNRAIAVEDDWRTFPRYA 122

Query: 145 AAPASIL---TIETKNLP-----IEQMDKL 166
           A   S     ++ TKNLP     +EQM  +
Sbjct: 123 AIGGSQKDNNSVLTKNLPDYYRELEQMKNM 152


  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
   0.319    0.135    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,489,900
Number of Sequences: 62578
Number of extensions: 148786
Number of successful extensions: 322
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 319
Number of HSP's gapped (non-prelim): 6
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
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: 48 (23.1 bits)