GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoA in Desulfovibrio vulgaris Hildenborough

Align 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase; 2-dehydro-3-deoxy-galactonate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase; EC 4.1.2.14; EC 4.1.2.51; EC 4.1.2.-; EC 4.1.2.21 (characterized)
to candidate 207334 DVU1868 dihydrodipicolinate synthase

Query= SwissProt::Q6KZI8
         (266 letters)



>MicrobesOnline__882:207334
          Length = 292

 Score =  105 bits (262), Expect = 1e-27
 Identities = 66/207 (31%), Positives = 108/207 (52%), Gaps = 8/207 (3%)

Query: 1   MITPLDAHGNIDYNATNILIKYLEGINVDYLFPMGSTGVFPYFTLKERKDFLKFVRENSK 60
           ++TP   +G +D      LI++     ++ L P G+TG     +  E +D ++   E  K
Sbjct: 10  IVTPF-RNGRVDEERFRELIEWQIEQGINGLVPCGTTGESATLSHDEHRDVIRICVEQVK 68

Query: 61  K--PIMAGVGSSSINEVNELMKFSMDIGIEAAVLMPPYYIKLNQEAIYHYYKEILSSNDM 118
              P++AG GS++  E  +L +F+ + G + A+L+ PYY K  QE +Y ++K I S   M
Sbjct: 69  GRIPVLAGAGSNNTREAIDLTRFAKEAGADGALLITPYYNKPTQEGLYLHFKAIASEVSM 128

Query: 119 DLLIYNIPQFT-NKIDPETVKNLKSEFSSVKGVKDSSADIRGFMEMLSLSDDDFAVFQGQ 177
             ++YN+P  T   I PET+  L  +   V GVK+++ ++    E+L     DF V  G 
Sbjct: 129 PFIVYNVPSRTGTNICPETLARLNRDIPEVVGVKEATGNLIQVSEILEYCGTDFQVLSGD 188

Query: 178 DDLLFTSLELGASGGVCGTTNFSDGIV 204
           D   FT L L + GG CG  + +  +V
Sbjct: 189 D---FTVLPLLSVGG-CGVISVTSNVV 211


Lambda     K      H
   0.319    0.139    0.400 

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: 174
Number of extensions: 9
Number of successful extensions: 3
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: 266
Length of database: 292
Length adjustment: 26
Effective length of query: 240
Effective length of database: 266
Effective search space:    63840
Effective search space used:    63840
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory