GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Phaeobacter inhibens BS107

Best path

deoP, deoK, deoC, adh, acs

Also see fitness data for the top candidates

Rules

Overview: Deoxyribose utilization in GapMind is based on MetaCyc pathways 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (link) and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (link).

19 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase PGA1_c34980
deoC deoxyribose-5-phosphate aldolase PGA1_c32790
adh acetaldehyde dehydrogenase (not acylating) PGA1_c32800 PGA1_c29650
acs acetyl-CoA synthetase, AMP-forming PGA1_c12950 PGA1_c11900
Alternative steps:
aacS acetoacetyl-CoA synthetase PGA1_262p01840 PGA1_c34070
ackA acetate kinase PGA1_c28840
ald-dh-CoA acetaldehyde dehydrogenase, acylating PGA1_c19350
atoA acetoacetyl-CoA transferase, A subunit PGA1_c06210
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
atoD acetoacetyl-CoA transferase, B subunit PGA1_c06200
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase PGA1_c08430 PGA1_c13170
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit PGA1_c09950 PGA1_c16210
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit PGA1_c09930
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase PGA1_c31360
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme PGA1_c08400
pta phosphate acetyltransferase PGA1_c28850

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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, 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