GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araD in Escherichia coli BW25113

Align L-ribulose-5-phosphate 4-epimerase SgbE; Phosphoribulose isomerase; EC 5.1.3.4 (characterized)
to candidate 17644 b3583 L-ribulose-5-phosphate 4-epimerase (NCBI)

Query= SwissProt::P37680
         (231 letters)



>FitnessBrowser__Keio:17644
          Length = 231

 Score =  476 bits (1226), Expect = e-139
 Identities = 231/231 (100%), Positives = 231/231 (100%)

Query: 1   MLEQLKADVLAANLALPAHHLVTFTWGNVSAVDETRQWMVIKPSGVEYDVMTADDMVVVE 60
           MLEQLKADVLAANLALPAHHLVTFTWGNVSAVDETRQWMVIKPSGVEYDVMTADDMVVVE
Sbjct: 1   MLEQLKADVLAANLALPAHHLVTFTWGNVSAVDETRQWMVIKPSGVEYDVMTADDMVVVE 60

Query: 61  IASGKVVEGSKKPSSDTPTHLALYRRYAEIGGIVHTHSRHATIWSQAGLDLPAWGTTHAD 120
           IASGKVVEGSKKPSSDTPTHLALYRRYAEIGGIVHTHSRHATIWSQAGLDLPAWGTTHAD
Sbjct: 61  IASGKVVEGSKKPSSDTPTHLALYRRYAEIGGIVHTHSRHATIWSQAGLDLPAWGTTHAD 120

Query: 121 YFYGAIPCTRQMTAEEINGEYEYQTGEVIIETFEERGRSPAQIPAVLVHSHGPFAWGKNA 180
           YFYGAIPCTRQMTAEEINGEYEYQTGEVIIETFEERGRSPAQIPAVLVHSHGPFAWGKNA
Sbjct: 121 YFYGAIPCTRQMTAEEINGEYEYQTGEVIIETFEERGRSPAQIPAVLVHSHGPFAWGKNA 180

Query: 181 ADAVHNAVVLEECAYMGLFSRQLAPQLPAMQNELLDKHYLRKHGANAYYGQ 231
           ADAVHNAVVLEECAYMGLFSRQLAPQLPAMQNELLDKHYLRKHGANAYYGQ
Sbjct: 181 ADAVHNAVVLEECAYMGLFSRQLAPQLPAMQNELLDKHYLRKHGANAYYGQ 231


Lambda     K      H
   0.318    0.132    0.405 

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: 359
Number of extensions: 8
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: 231
Length of database: 231
Length adjustment: 23
Effective length of query: 208
Effective length of database: 208
Effective search space:    43264
Effective search space used:    43264
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 (21.7 bits)
S2: 46 (22.3 bits)

Align candidate 17644 b3583 (L-ribulose-5-phosphate 4-epimerase (NCBI))
to HMM TIGR00760 (araD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.1991.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1991.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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