GapMind for catabolism of small carbon sources

 

thymidine catabolism in Belnapia rosea CPCC 100156

Best path

nupC, deoA, deoB, deoC, adh, acs

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 (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupC thymidine permease NupC BLR02_RS12095
deoA thymidine phosphorylase DeoA
deoB phosphopentomutase BLR02_RS26050 BLR02_RS24035
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) BLR02_RS07320 BLR02_RS18460
acs acetyl-CoA synthetase, AMP-forming BLR02_RS09295 BLR02_RS17730
Alternative steps:
ackA acetate kinase BLR02_RS16785
ald-dh-CoA acetaldehyde dehydrogenase, acylating
nupG thymidine permease NupG/XapB
pta phosphate acetyltransferase BLR02_RS16780 BLR02_RS20655
Slc28a3 thymidine:Na+ symporter SLC28A3 BLR02_RS12095
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 Sep 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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