GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolE in Pseudomonas fluorescens FW300-N2E2

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate Pf6N2E2_513 Inosose dehydratase (EC 4.2.1.44)

Query= reanno::pseudo6_N2E2:Pf6N2E2_513
         (297 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_513
          Length = 297

 Score =  602 bits (1552), Expect = e-177
 Identities = 297/297 (100%), Positives = 297/297 (100%)

Query: 1   MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLR 60
           MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLR
Sbjct: 1   MPAIRIGINPISWSNDDLPSLGGETPLSTALSEGKAIGYEGFELNGKFPKDAKGVGDVLR 60

Query: 61  PYDLALVSGWYSSRLARRSAAEEIDAIASHVELLAQNGATVLVYGEVADSIQGQRIALIE 120
           PYDLALVSGWYSSRLARRSAAEEIDAIASHVELLAQNGATVLVYGEVADSIQGQRIALIE
Sbjct: 61  PYDLALVSGWYSSRLARRSAAEEIDAIASHVELLAQNGATVLVYGEVADSIQGQRIALIE 120

Query: 121 RPRFHTDEAWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL 180
           RPRFHTDEAWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL
Sbjct: 121 RPRFHTDEAWQAYADKLTELARFTLSQGVRLAYHHHMGAYVESPADIDKLMALTGSEVGL 180

Query: 181 LFDSGHCYMGGGEPLQVLRKHIERICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240
           LFDSGHCYMGGGEPLQVLRKHIERICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP
Sbjct: 181 LFDSGHCYMGGGEPLQVLRKHIERICHVHFKDVRKPVVQLARNNLWSFPDCIINGTFTVP 240

Query: 241 GDGDIDFAALLDVLLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRALLQERNPS 297
           GDGDIDFAALLDVLLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRALLQERNPS
Sbjct: 241 GDGDIDFAALLDVLLAADYQGWLVVEAEQDPAVAPSYAYAKKGYDTLRALLQERNPS 297


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: 460
Number of extensions: 14
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: 297
Length of database: 297
Length adjustment: 26
Effective length of query: 271
Effective length of database: 271
Effective search space:    73441
Effective search space used:    73441
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 Pf6N2E2_513 (Inosose dehydratase (EC 4.2.1.44))
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))

Software error:

../bin/blast/fastacmd -i /tmp/list.11044.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11044.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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