GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Escherichia coli BW25113

Align 1-phosphofructokinase (characterized)
to candidate 16277 b2168 1-phosphofructokinase (NCBI)

Query= CharProtDB::CH_024159
         (312 letters)



>FitnessBrowser__Keio:16277
          Length = 312

 Score =  621 bits (1602), Expect = 0.0
 Identities = 312/312 (100%), Positives = 312/312 (100%)

Query: 1   MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGG 60
           MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGG
Sbjct: 1   MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGG 60

Query: 61  FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWER 120
           FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWER
Sbjct: 61  FLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWER 120

Query: 121 FVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA 180
           FVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA
Sbjct: 121 FVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAA 180

Query: 181 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIA 240
           PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIA
Sbjct: 181 PWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIA 240

Query: 241 KPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLA 300
           KPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLA
Sbjct: 241 KPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLA 300

Query: 301 AMMARVDLQPFN 312
           AMMARVDLQPFN
Sbjct: 301 AMMARVDLQPFN 312


Lambda     K      H
   0.319    0.135    0.404 

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: 520
Number of extensions: 9
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: 312
Length of database: 312
Length adjustment: 27
Effective length of query: 285
Effective length of database: 285
Effective search space:    81225
Effective search space used:    81225
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 16277 b2168 (1-phosphofructokinase (NCBI))
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

Software error:

../bin/blast/fastacmd -i /tmp/list.13924.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13924.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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