thymidine catabolism in Yersinia intermedia Y228

GapMind for catabolism of small carbon sources

thymidine catabolism in Yersinia intermedia Y228

Best path

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.

all: thymidine-transport, deoA, deoB, deoC and acetaldehyde-degradation

Comment: After the phosphorylase deoA forms deoxyribose 1-phosphate, a phosphopentomutase forms deoxyribose-5-phosphate, and an aldolase yields glyceraldehyde 3-phosphate (an intermediate in glycolysis) and acetaldehyde.

acetaldehyde-degradation:

ald-dh-CoA
or adh and acs
or adh, ackA and pta
Comment: Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA by either acetyl-CoA synthetase (acs) or by acetate kinase (ackA) and phosphate acetyltransferase (pta).

thymidine-transport:

nupG
or Slc29a1
or nupC
or Slc28a3
Comment: Transporters were identified using query: transporter:thymidine:deoxythymidine

12 steps (11 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
nupG	thymidine permease NupG/XapB	CH53_RS16770
deoA	thymidine phosphorylase DeoA	CH53_RS05550	CH53_RS10175
deoB	phosphopentomutase	CH53_RS05545
deoC	deoxyribose-5-phosphate aldolase	CH53_RS05555	CH53_RS01050
ald-dh-CoA	acetaldehyde dehydrogenase, acylating	CH53_RS19095	CH53_RS12405
Alternative steps:
ackA	acetate kinase	CH53_RS01940	CH53_RS21405
acs	acetyl-CoA synthetase, AMP-forming	CH53_RS07140
adh	acetaldehyde dehydrogenase (not acylating)	CH53_RS19095	CH53_RS18425
nupC	thymidine permease NupC	CH53_RS02535	CH53_RS09090
pta	phosphate acetyltransferase	CH53_RS01945	CH53_RS12390
Slc28a3	thymidine:Na+ symporter SLC28A3	CH53_RS05560	CH53_RS13865
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources