GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas fluorescens FW300-N2E3

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase AO353_20835
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) AO353_22390 AO353_06560
ackA acetate kinase AO353_04410
pta phosphate acetyltransferase AO353_05065
Alternative steps:
aacS acetoacetyl-CoA synthetase AO353_21765 AO353_20355
acs acetyl-CoA synthetase, AMP-forming AO353_03060 AO353_14365
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit AO353_27935
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
atoD acetoacetyl-CoA transferase, B subunit AO353_27940
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase AO353_24520 AO353_21770
deoxyribonate-transport 2-deoxy-D-ribonate transporter AO353_29035 AO353_24515
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit AO353_01425 AO353_23430
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit AO353_23435 AO353_01420
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component AO353_10800 AO353_27065
garK glycerate 2-kinase AO353_01935 AO353_26900
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme AO353_07745

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