GapMind for catabolism of small carbon sources

 

thymidine catabolism in Desulfobacter vibrioformis DSM 8776

Best path

nupC, deoA, deoB, deoC, adh, ackA, pta

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 (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nupC thymidine permease NupC Q366_RS09940
deoA thymidine phosphorylase DeoA Q366_RS01905
deoB phosphopentomutase
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) Q366_RS11495 Q366_RS17050
ackA acetate kinase Q366_RS12110
pta phosphate acetyltransferase Q366_RS09670 Q366_RS07670
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming Q366_RS12130 Q366_RS06190
ald-dh-CoA acetaldehyde dehydrogenase, acylating Q366_RS10690
nupG thymidine permease NupG/XapB
Slc28a3 thymidine:Na+ symporter SLC28A3 Q366_RS09940
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 Apr 09 2024. 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