GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas putida KT2440

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 PP_3621 PP_2477
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit PP_3622 PP_2478
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component PP_3623 PP_3382
deoxyribonate-transport 2-deoxy-D-ribonate transporter PP_2830 PP_4758
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase PP_2784 PP_1946
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme PP_0303
garK glycerate 2-kinase PP_4300 PP_3178
atoA acetoacetyl-CoA transferase, A subunit PP_3122 PP_3951
atoD acetoacetyl-CoA transferase, B subunit PP_3123 PP_3952
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
Alternative steps:
aacS acetoacetyl-CoA synthetase PP_3071 PP_3458
ackA acetate kinase PP_1457
acs acetyl-CoA synthetase, AMP-forming PP_4487 PP_4702
adh acetaldehyde dehydrogenase (not acylating) PP_2680 PP_0545
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase PP_2458 PP_4934
deoP deoxyribose transporter
pta phosphate acetyltransferase PP_0774

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