GapMind for catabolism of small carbon sources

 

Protein 15740 in Escherichia coli BW25113

Annotation: b1619 7-alpha-hydroxysteroid dehydrogenase (NCBI)

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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