GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Phaeobacter inhibens BS107

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF3394 PGA1_c34470 UDP-glucose 4-epimerase ExoB

Query= curated2:Q59745
         (327 letters)



>FitnessBrowser__Phaeo:GFF3394
          Length = 327

 Score =  330 bits (847), Expect = 2e-95
 Identities = 163/317 (51%), Positives = 215/317 (67%), Gaps = 1/317 (0%)

Query: 6   VLVVGGAGYIGSHTCLDLANKGYRPVVFDNFSNGHREFVRWGPAEEGDIRDRARLDEVLA 65
           +LV GGAGYIGSH C  L   G+ PV +DN   G ++ V++GP E+GD+ DRARLDEV A
Sbjct: 4   ILVTGGAGYIGSHACKALRAAGFTPVTYDNLVTGWQDAVKFGPFEKGDLSDRARLDEVFA 63

Query: 66  KHKPAAILHFAALIEVGESVKDPVSFYENNVIGTLTLLSAAQAAGINAFVFSSTCATYGL 125
           K++PAA++HFAAL +VGE++ +P  ++ NNV G+LTL+ AA AA    FVFSSTCATYG 
Sbjct: 64  KYQPAAVMHFAALSQVGEAMSEPGRYWANNVGGSLTLIEAAVAADCLDFVFSSTCATYGE 123

Query: 126 PQSVPLDETHRQVPINPYGRTKYIVEQALADYDQYGSLRSVVLRYFNAAGADFEGRIGEW 185
             +V LDE+  QVP+N YG +K  VE  L D+     LRSV+ RYFN AGAD E  +GE+
Sbjct: 124 HDNVVLDESTPQVPLNAYGASKRAVEDILRDFGASHGLRSVIFRYFNVAGADPEAEVGEF 183

Query: 186 HQPETHAIPLAIDAALGRRQGFKVFGSDYETRDGTCVRDYIHVLDLADAHVRAVEYLLKG 245
           H+PETH +PL +DA  G+R    +FG+DY+T DGTCVRDY+HV DL DAHV  +++L  G
Sbjct: 184 HRPETHLVPLVLDAIDGKRDALTIFGTDYDTPDGTCVRDYVHVCDLVDAHVLGLKWLKDG 243

Query: 246 GDSVALNLGTGTGTTVKELLGAIEEVSNRPFPVEYIGRREGDSHTLVANNDKARDVLGWV 305
             S   NLGTGTG +V+E++   E  + +  P     RR GD   LV+ + +A  +LGW 
Sbjct: 244 KGSQVFNLGTGTGFSVREVMDKAEATTGKSVPHSIGPRRAGDCTKLVSGSVRAATLLGWE 303

Query: 306 P-QYDLSEIIRSAWDWH 321
           P + DL  +I  AW WH
Sbjct: 304 PTRSDLETMIADAWGWH 320


Lambda     K      H
   0.319    0.137    0.415 

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: 383
Number of extensions: 13
Number of successful extensions: 2
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: 327
Length of database: 327
Length adjustment: 28
Effective length of query: 299
Effective length of database: 299
Effective search space:    89401
Effective search space used:    89401
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate GFF3394 PGA1_c34470 (UDP-glucose 4-epimerase ExoB)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.17355.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17355.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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