GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Marinobacter adhaerens HP15

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF2094 HP15_2048 UDP-glucose 4-epimerase

Query= curated2:Q59083
         (348 letters)



>FitnessBrowser__Marino:GFF2094
          Length = 342

 Score =  349 bits (895), Expect = e-101
 Identities = 180/319 (56%), Positives = 221/319 (69%), Gaps = 1/319 (0%)

Query: 10  RVLVTGGAGYIGSHVLHALTDAGIPAVTIDDLSAGRREAIPAAVPLVEGDIGSAELLDRV 69
           +VLVTGGAGYIGSHV+  L  AG   V  D+LS G R A+ A   LV GD+     ++ +
Sbjct: 2   KVLVTGGAGYIGSHVVRQLGQAGHDIVVFDNLSTGYRWAVTAG-ELVVGDLADEAAIEDL 60

Query: 70  MRDHRVDAVMHFAGSIVVPESVVKPLDYYRNNTANSLTLLGACLRAGIDKVVFSSTAAVY 129
              H+ +AV+HFA +IVVPESV  PL YY NNT N+L LL A  +  +  +VFSSTAAVY
Sbjct: 61  FSRHQFEAVLHFAANIVVPESVANPLKYYSNNTRNTLNLLKAVEKHEVPYMVFSSTAAVY 120

Query: 130 GAPESVPIREDAPTVPINPYGASKLMTEQMLRDAGAAHGLRSVILRYFNVAGADPAGRTG 189
           G PE   + ED P  PINPYGASK+M+E+M+ D  AA  L  VILRYFNVAGA+P G  G
Sbjct: 121 GMPEQTVLTEDLPLAPINPYGASKMMSERMIMDLAAASSLNYVILRYFNVAGANPEGLLG 180

Query: 190 QATPVATHLIKVACQALLGRRPPLAIFGTDYDTPDGTCIRDYIHVSDLADAHVLALLHLR 249
           QATP ATHLIKVAC+ +  +R  +++FGTDYDT DGTCIRDYIHV DLA AHV+AL ++ 
Sbjct: 181 QATPEATHLIKVACECVTEQREGMSVFGTDYDTRDGTCIRDYIHVEDLAKAHVMALDYMA 240

Query: 250 RGGGSLLMNCGYGRGASVREVVRTLEEVSGEQVPATFADRRPGDPPQLVAGADRIREQLG 309
            GG S +MNCGYGRG +VREV+  ++  SG   P T   RR GDP  L+A    IR+ LG
Sbjct: 241 DGGHSKVMNCGYGRGFTVREVIDVVKAQSGVDFPVTETGRRAGDPAALMADNTLIRQTLG 300

Query: 310 WVPKHDRLDGIVRSALSWE 328
           W P +D LD IV +AL+WE
Sbjct: 301 WQPDYDNLDTIVGTALAWE 319


Lambda     K      H
   0.319    0.136    0.401 

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: 364
Number of extensions: 12
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: 348
Length of database: 342
Length adjustment: 29
Effective length of query: 319
Effective length of database: 313
Effective search space:    99847
Effective search space used:    99847
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: 49 (23.5 bits)

Align candidate GFF2094 HP15_2048 (UDP-glucose 4-epimerase)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.20055.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20055.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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