GapMind for catabolism of small carbon sources

 

Protein 15740 in Escherichia coli BW25113

Annotation: FitnessBrowser__Keio:15740

Length: 255 amino acids

Source: Keio in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 35% 96% 142.9 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 91% 134 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 91% 134 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 91% 134 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 32% 94% 118.2 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 32% 94% 118.2 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 31% 96% 108.2 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 33% 55% 103.6 7-alpha-hydroxysteroid dehydrogenase; EC 1.1.1.159 100% 499.6

Sequence Analysis Tools

View 15740 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

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Sequence

MFNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGG
QAFACRCDITSEQELSALADFAISKLGKVDILVNNAGGGGPKPFDMPMADFRRAYELNVF
SFFHLSQLVAPEMEKNGGGVILTITSMAAENKNINMTSYASSKAAASHLVRNMAFDLGEK
NIRVNGIAPGAILTDALKSVITPEIEQKMLQHTPIRRLGQPQDIANAALFLCSPAASWVS
GQILTVSGGGVQELN

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