GapMind for catabolism of small carbon sources

 

thymidine catabolism in Acidovorax sp. GW101-3H11

Best path

nupG, deoA, deoB, deoC, adh, acs

Also see fitness data for the top candidates

Rules

Overview: Thymidine degradation in GapMind is based on thymidine phoshorylase (EC 2.4.2.4), which yields 2-deoxyribose-1-phosphate and thymine. The catabolism of thymine is not represented, as it may be excreted.

12 steps (6 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupG thymidine permease NupG/XapB
deoA thymidine phosphorylase DeoA Ac3H11_2202 Ac3H11_2615
deoB phosphopentomutase Ac3H11_444
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
acs acetyl-CoA synthetase, AMP-forming Ac3H11_951 Ac3H11_191
Alternative steps:
ackA acetate kinase Ac3H11_4666
ald-dh-CoA acetaldehyde dehydrogenase, acylating
nupC thymidine permease NupC
pta phosphate acetyltransferase Ac3H11_1079 Ac3H11_4331
Slc28a3 thymidine:Na+ symporter SLC28A3
Slc29a1 thymidine transporter Slc29a1

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 Aug 02 2021. The underlying query database was built on Aug 02 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