GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Shewanella amazonensis SB2B

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 Sama_0562 Sama_1663
deoK deoxyribokinase
deoC deoxyribose-5-phosphate aldolase Sama_0973
adh acetaldehyde dehydrogenase (not acylating) Sama_3435 Sama_1693
ackA acetate kinase Sama_1495 Sama_2807
pta phosphate acetyltransferase Sama_1494
Alternative steps:
aacS acetoacetyl-CoA synthetase Sama_1904 Sama_2897
acs acetyl-CoA synthetase, AMP-forming Sama_2079 Sama_1364
ald-dh-CoA acetaldehyde dehydrogenase, acylating Sama_1693
atoA acetoacetyl-CoA transferase, A subunit Sama_0518 Sama_1357
atoB acetyl-CoA C-acetyltransferase Sama_1375 Sama_0031
atoD acetoacetyl-CoA transferase, B subunit Sama_1356 Sama_0519
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase Sama_0517 Sama_0389
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit Sama_3438
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit Sama_3439
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase Sama_3228
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