GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Escherichia coli BW25113

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 18404 b4383 phosphopentomutase (NCBI)

Query= BRENDA::P0A6K6
         (407 letters)



>FitnessBrowser__Keio:18404
          Length = 407

 Score =  839 bits (2168), Expect = 0.0
 Identities = 407/407 (100%), Positives = 407/407 (100%)

Query: 1   MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG 60
           MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG
Sbjct: 1   MKRAFIMVLDSFGIGATEDAERFGDVGADTLGHIAEACAKGEADNGRKGPLNLPNLTRLG 60

Query: 61  LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH 120
           LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH
Sbjct: 61  LAKAHEGSTGFIPAGMDGNAEVIGAYAWAHEMSSGKDTPSGHWEIAGVPVLFEWGYFSDH 120

Query: 121 ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC 180
           ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC
Sbjct: 121 ENSFPQELLDKLVERANLPGYLGNCHSSGTVILDQLGEEHMKTGKPIFYTSADSVFQIAC 180

Query: 181 HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP 240
           HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP
Sbjct: 181 HEETFGLDKLYELCEIAREELTNGGYNIGRVIARPFIGDKAGNFQRTGNRHDLAVEPPAP 240

Query: 241 TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT 300
           TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT
Sbjct: 241 TVLQKLVDEKHGQVVSVGKIADIYANCGITKKVKATGLDALFDATIKEMKEAGDNTIVFT 300

Query: 301 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT 360
           NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT
Sbjct: 301 NFVDFDSSWGHRRDVAGYAAGLELFDRRLPELMSLLRDDDILILTADHGCDPTWTGTDHT 360

Query: 361 REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAMF 407
           REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAMF
Sbjct: 361 REHIPVLVYGPKVKPGSLGHRETFADIGQTLAKYFGTSDMEYGKAMF 407


Lambda     K      H
   0.318    0.138    0.422 

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: 847
Number of extensions: 31
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: 407
Length of database: 407
Length adjustment: 31
Effective length of query: 376
Effective length of database: 376
Effective search space:   141376
Effective search space used:   141376
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: 50 (23.9 bits)

Align candidate 18404 b4383 (phosphopentomutase (NCBI))
to HMM TIGR01696 (deoB: phosphopentomutase (EC 5.4.2.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.8234.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8234.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.