GapMind for catabolism of small carbon sources

 

thymidine catabolism in Pseudomonas putida KT2440

Best path

nupG, deoA, deoB, deoC, adh, ackA, pta

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 PP_4248
deoB phosphopentomutase PP_4716
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) PP_2680 PP_0545
ackA acetate kinase PP_1457
pta phosphate acetyltransferase PP_0774
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming PP_4487 PP_4702
ald-dh-CoA acetaldehyde dehydrogenase, acylating
nupC thymidine permease NupC
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