GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_6031 Pf1N1B4_405
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) Pf1N1B4_4502 Pf1N1B4_2673
ackA acetate kinase Pf1N1B4_879
pta phosphate acetyltransferase Pf1N1B4_1055
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf1N1B4_5634 Pf1N1B4_3988
acs acetyl-CoA synthetase, AMP-forming Pf1N1B4_3430 Pf1N1B4_2849
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit Pf1N1B4_5833
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
atoD acetoacetyl-CoA transferase, B subunit Pf1N1B4_5834
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Pf1N1B4_5039 Pf1N1B4_4556
deoxyribonate-transport 2-deoxy-D-ribonate transporter Pf1N1B4_5692 Pf1N1B4_4622
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit Pf1N1B4_4870 Pf1N1B4_465
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit Pf1N1B4_4584 Pf1N1B4_4869
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase Pf1N1B4_3658 Pf1N1B4_4998
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme Pf1N1B4_2430

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 Aug 02 2021. The underlying query database was built on Aug 02 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