GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Bacteroides thetaiotaomicron VPI-5482

Align UDP-glucose 4-epimerase; EC 5.1.3.2 (characterized, see rationale)
to candidate 350151 BT0623 putative UDP-glucose 4-epimerase (NCBI ptt file)

Query= uniprot:L0FXG3
         (337 letters)



>FitnessBrowser__Btheta:350151
          Length = 344

 Score =  399 bits (1024), Expect = e-116
 Identities = 196/338 (57%), Positives = 256/338 (75%), Gaps = 2/338 (0%)

Query: 2   QQILITGGAGYIGSHTAVALVNAGYEPIIVDNFSNSNKEVLNGLEKILGAPVKYHEGDCN 61
           ++IL+TGG GYIGSHT V L N+GYE II+DN SNS+ +V++ +EK+ G    + + DC 
Sbjct: 3   ERILVTGGTGYIGSHTVVELQNSGYEVIIIDNLSNSSADVVDNIEKVSGIRPAFEKLDCL 62

Query: 62  DRKFMQAVFEE-NDLQGVIHFAASKAVGESTKIPLTYYSNNINSLIILLETMKQFGVKDI 120
           D   + AVF +   ++ +IHFAASKAVGES + PL YY NN+ SLI LLE M + GV+ I
Sbjct: 63  DFAGLDAVFAKYKGIKAIIHFAASKAVGESVEKPLLYYRNNLVSLINLLELMPKHGVEGI 122

Query: 121 VFSSSCTVYGQPDKLPVKETTPRKDAESPYGNTKKICEDILTDHVKSGAPARVVALRYFN 180
           VFSSSCTVYGQPD+LPV E  P K AESPYGNTK+I E+I+ D + SGAP   + LRYFN
Sbjct: 123 VFSSSCTVYGQPDELPVTEKAPIKKAESPYGNTKQINEEIIRDTIASGAPINAILLRYFN 182

Query: 181 PIGAHPSSLIGELPLGVPANLIPFVTQTGAGIREKITVFGDDYNTPDGTCIRDYIHVMDL 240
           PIGAHP++L+GELP GVP NLIP++TQT  GIREK++VFGDDY+TPDG+CIRD+I+V+DL
Sbjct: 183 PIGAHPTALLGELPNGVPQNLIPYLTQTAMGIREKLSVFGDDYDTPDGSCIRDFINVVDL 242

Query: 241 ADAHVKSIQYLADQPE-NFIDLFNVGTGNGNTVMEVIKAFEKVSEKPLNYEIGPRRSGDI 299
           A AHV +I+ + +Q +   +++FN+GTG G +V+E+I  FEK +   LNY+I  RR+GDI
Sbjct: 243 AKAHVIAIRRILEQKQKEKVEVFNIGTGRGVSVLELINGFEKATGVKLNYQIVGRRAGDI 302

Query: 300 EKVWANTDKVSKVLGWTPQFGLEEALRDAWNWQLSLKK 337
           EKVWAN D  ++ LGW     LE+ LR AWNWQL L++
Sbjct: 303 EKVWANPDYANQELGWKAVETLEDTLRSAWNWQLKLRE 340


Lambda     K      H
   0.316    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 413
Number of extensions: 12
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 337
Length of database: 344
Length adjustment: 28
Effective length of query: 309
Effective length of database: 316
Effective search space:    97644
Effective search space used:    97644
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 350151 BT0623 (putative UDP-glucose 4-epimerase (NCBI ptt file))
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.12554.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12554.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.