GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1905 Pf6N2E2_1203
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit Pf6N2E2_1904 Pf6N2E2_1204
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component Pf6N2E2_1903 Pf6N2E2_4408
deoxyribonate-transport 2-deoxy-D-ribonate transporter Pf6N2E2_1105 Pf6N2E2_2115
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Pf6N2E2_1375 Pf6N2E2_1663
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme Pf6N2E2_4692
garK glycerate 2-kinase Pf6N2E2_5836 Pf6N2E2_460
atoA acetoacetyl-CoA transferase, A subunit Pf6N2E2_2111
atoD acetoacetyl-CoA transferase, B subunit Pf6N2E2_2112
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf6N2E2_2042 Pf6N2E2_2190
ackA acetate kinase Pf6N2E2_5444
acs acetyl-CoA synthetase, AMP-forming Pf6N2E2_5659 Pf6N2E2_5149
adh acetaldehyde dehydrogenase (not acylating) Pf6N2E2_1381 Pf6N2E2_4979
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase Pf6N2E2_165
deoP deoxyribose transporter
pta phosphate acetyltransferase Pf6N2E2_5260

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