GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas fluorescens GW456-L13

Best path

deoP, deoK, deoC, adh, ackA, pta

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase PfGW456L13_3908
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) PfGW456L13_3517 PfGW456L13_1342
ackA acetate kinase PfGW456L13_4820
pta phosphate acetyltransferase PfGW456L13_4990
Alternative steps:
aacS acetoacetyl-CoA synthetase PfGW456L13_2872 PfGW456L13_2593
acs acetyl-CoA synthetase, AMP-forming PfGW456L13_1963 PfGW456L13_1517
ald-dh-CoA acetaldehyde dehydrogenase, acylating PfGW456L13_2505
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase PfGW456L13_3458 PfGW456L13_2058
deoxyribonate-transport 2-deoxy-D-ribonate transporter PfGW456L13_3929 PfGW456L13_2481
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit PfGW456L13_2091 PfGW456L13_3353
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit PfGW456L13_3352 PfGW456L13_2092
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component PfGW456L13_3925
garK glycerate 2-kinase PfGW456L13_4298 PfGW456L13_2941
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme PfGW456L13_1095

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, 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