GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Escherichia coli BW25113

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate 14472 b0334 2-methylcitrate dehydratase (NCBI)

Query= BRENDA::P77243
         (483 letters)



>FitnessBrowser__Keio:14472
          Length = 483

 Score =  971 bits (2510), Expect = 0.0
 Identities = 483/483 (100%), Positives = 483/483 (100%)

Query: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL
Sbjct: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60

Query: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180
           LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST
Sbjct: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180

Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK
Sbjct: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240

Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA
Sbjct: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360
           MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR
Sbjct: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360

Query: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420
           LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV
Sbjct: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420

Query: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480
           VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL
Sbjct: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480

Query: 481 YVI 483
           YVI
Sbjct: 481 YVI 483


Lambda     K      H
   0.321    0.136    0.406 

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: 935
Number of extensions: 17
Number of successful extensions: 1
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 14472 b0334 (2-methylcitrate dehydratase (NCBI))
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

Software error:

../bin/blast/fastacmd -i /tmp/list.31142.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31142.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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