GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Pseudomonas simiae WCS417

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 PS417_10890 PS417_13030
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit PS417_10885
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component PS417_10880 PS417_00270
deoxyribonate-transport 2-deoxy-D-ribonate transporter PS417_07260 PS417_07265
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase PS417_07245 PS417_11520
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme PS417_07250 PS417_26280
garK glycerate 2-kinase PS417_13970 PS417_08795
atoA acetoacetyl-CoA transferase, A subunit PS417_10525
atoD acetoacetyl-CoA transferase, B subunit PS417_10520
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
Alternative steps:
aacS acetoacetyl-CoA synthetase PS417_12145 PS417_17010
ackA acetate kinase PS417_22945
acs acetyl-CoA synthetase, AMP-forming PS417_21750 PS417_23925
adh acetaldehyde dehydrogenase (not acylating) PS417_17430 PS417_24810
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase PS417_18385 PS417_21365
deoP deoxyribose transporter
pta phosphate acetyltransferase PS417_03730

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