GapMind for catabolism of small carbon sources

 

Definition of thymidine catabolism

As text, or see rules and steps

# 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.

nupG	thymidine permease NupG/XapB	curated:CharProtDB::CH_088596	curated:SwissProt::P45562

# Transporters were identified using
# query: transporter:thymidine:deoxythymidine
thymidine-transport: nupG

Slc29a1	thymidine transporter Slc29a1	curated:SwissProt::O54698
thymidine-transport: Slc29a1

# A nupC-like protein from Shewanella sp. ANA-3 (Shewana3_1039, A0KU05)
# is important for utilization of thymidine and other nucleosides.
# A similar protein from V. cholerae (uniprot:Q9KPL5) binds uridine and 2'-deoxyuridine and
# is likely to be a thymidine transporter as well, but this is not proven.
# The nupC protein from B. subtilis (P39141) was shown to be a uridine transporter (PMID:8550462)
# and is suspected to be a thymidine transporter as well, so it is ignored.
# The specificity of E. coli nupX (P33021, also known as yeiJ) seems to be unknown.
nupC	thymidine permease NupC	curated:SwissProt::P0AFF2	ignore:SwissProt::P39141	uniprot:A0KU05	ignore:TCDB::Q9KPL5	ignore:SwissProt::P33021
thymidine-transport: nupC

Slc28a3	thymidine:Na+ symporter SLC28A3	curated:TCDB::Q9UA35
thymidine-transport: Slc28a3

# A non-specific lysosomal transporter (TC 2.A.74.1.1 / Q60961) was ignored

# P19663 is ignored because it is a sequence fragment.
# Many uridine phosphorylases (EC:2.4.2.3) are also deoxyuridine phosphorylases and thymidine phosphyrylases, so
# hits to these are ignored.
deoA	thymidine phosphorylase DeoA	EC:2.4.2.2	EC:2.4.2.4	ignore:SwissProt::P19663	ignore_other:2.4.2.3

import deoxyinosine.steps:deoB # phosphopentomutase

import deoxyribose.steps:deoC # deoxyribose-5-phosphate aldolase

import ethanol.steps:acetaldehyde-degradation

# 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.
all: thymidine-transport deoA deoB deoC acetaldehyde-degradation

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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