GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Sinorhizobium meliloti 1021

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase SMc01103 SMc03138
deoC deoxyribose-5-phosphate aldolase SM_b21300 SMc02333
adh acetaldehyde dehydrogenase (not acylating) SM_b21301 SM_b21539
ackA acetate kinase SM_b21184
pta phosphate acetyltransferase SM_b21532 SMc01126
Alternative steps:
aacS acetoacetyl-CoA synthetase SMc00774 SMc02162
acs acetyl-CoA synthetase, AMP-forming SMc04093 SMc04095
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase SMc02041 SMc00372
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit SMa1491 SM_b20343
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit SMa1488 SM_b20342
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component SM_b20402 SMc00086
garK glycerate 2-kinase SM_b20678 SMc04389
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme SMc01637

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