GapMind for catabolism of small carbon sources

 

Protein 201628 in Shewanella oneidensis MR-1

Annotation: FitnessBrowser__MR1:201628

Length: 608 amino acids

Source: MR1 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-cellobiose catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-gluconate catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-gluconate catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-glucose catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-glucose catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
lactose catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
lactose catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-maltose catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
D-maltose catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
sucrose catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
sucrose catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
trehalose catabolism edd hi phosphogluconate dehydratase (characterized) 67% 99% 806.6 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
trehalose catabolism edd hi edd: phosphogluconate dehydratase (EC 4.2.1.12) (TIGR01196) 100% 1027.5 dihydroxy-acid dehydratase (EC 4.2.1.9) 31% 223.8
L-arabinose catabolism xacD lo L-arabonate dehydratase (EC 4.2.1.25) (characterized) 31% 84% 218 phosphogluconate dehydratase 67% 806.6
D-galactose catabolism dgoD lo L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized) 30% 89% 213 phosphogluconate dehydratase 67% 806.6
lactose catabolism dgoD lo L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized) 30% 89% 213 phosphogluconate dehydratase 67% 806.6
D-xylose catabolism xad lo xylonate dehydratase (EC 4.2.1.82) (characterized) 31% 79% 182.2 phosphogluconate dehydratase 67% 806.6

Sequence Analysis Tools

View 201628 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MHSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACNPDDKNAL
RQLTKANIGIITAFNDMLSAHQPYETYPDLLKKACQEVGSVAQVAGGVPAMCDGVTQGQP
GMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGP
MKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGLQ
LPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGS
TNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKEL
LDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGL
KLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPK
ANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQD
GDLIRVDALTGELSLLVSDTELATRTATEIDLRHSRYGMGRELFGVLRSNLSSPETGARS
TSAIDELY

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

Links

Downloads

Related tools

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