GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Shewanella loihica PV-4

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 Shew_0696
deoC deoxyribose-5-phosphate aldolase Shew_2815
adh acetaldehyde dehydrogenase (not acylating) Shew_3574 Shew_1910
ackA acetate kinase Shew_2393
pta phosphate acetyltransferase Shew_2394
Alternative steps:
aacS acetoacetyl-CoA synthetase Shew_2593
acs acetyl-CoA synthetase, AMP-forming Shew_1533 Shew_2568
ald-dh-CoA acetaldehyde dehydrogenase, acylating Shew_1910
atoA acetoacetyl-CoA transferase, A subunit Shew_2575
atoB acetyl-CoA C-acetyltransferase Shew_1667 Shew_0018
atoD acetoacetyl-CoA transferase, B subunit Shew_2576
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Shew_2863 Shew_1407
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit Shew_2266
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit Shew_2265
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase Shew_2534
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme

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