GapMind for catabolism of small carbon sources

 

thymidine catabolism in Burkholderia phytofirmans PsJN

Best path

nupC, 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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupC thymidine permease NupC BPHYT_RS21960
deoA thymidine phosphorylase DeoA BPHYT_RS33245
deoB phosphopentomutase BPHYT_RS14155
deoC deoxyribose-5-phosphate aldolase BPHYT_RS25815
adh acetaldehyde dehydrogenase (not acylating) BPHYT_RS25810 BPHYT_RS00120
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHYT_RS07245 BPHYT_RS21770
nupG thymidine permease NupG/XapB
Slc28a3 thymidine:Na+ symporter SLC28A3 BPHYT_RS21960
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