GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Caulobacter crescentus NA1000

Best path

deoP, deoK, deoC, adh, acs

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase CCNA_01001
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) CCNA_03695 CCNA_03242
acs acetyl-CoA synthetase, AMP-forming CCNA_03696 CCNA_01889
Alternative steps:
aacS acetoacetyl-CoA synthetase CCNA_01017 CCNA_01382
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit CCNA_00206 CCNA_02488
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
atoD acetoacetyl-CoA transferase, B subunit CCNA_00207 CCNA_02489
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase CCNA_01892 CCNA_03172
deoxyribonate-transport 2-deoxy-D-ribonate transporter CCNA_02439
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit CCNA_00022 CCNA_02353
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit CCNA_02352 CCNA_00021
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase CCNA_03663 CCNA_02704

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