GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

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
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit AO356_30215 AO356_26895
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit AO356_30210 AO356_26900
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component AO356_30205
deoxyribonate-transport 2-deoxy-D-ribonate transporter AO356_26160 AO356_01235
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase AO356_27985 AO356_28740
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme AO356_13850
garK glycerate 2-kinase AO356_19605 AO356_22870
atoA acetoacetyl-CoA transferase, A subunit AO356_21650
atoD acetoacetyl-CoA transferase, B subunit AO356_21645
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
Alternative steps:
aacS acetoacetyl-CoA synthetase AO356_00425 AO356_01575
ackA acetate kinase AO356_17605
acs acetyl-CoA synthetase, AMP-forming AO356_18695 AO356_16045
adh acetaldehyde dehydrogenase (not acylating) AO356_28025 AO356_15225
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase AO356_00950
deoP deoxyribose transporter
pta phosphate acetyltransferase AO356_16680

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