Definition of D-serine catabolism
As rules and steps, or see full text
Rules
Overview: D-serine degradation in GapMind is based on the MetaCyc pathway (link)
- all: D-serine-transport and dsdA
- Comment: The ammonia-lyase (dsdA) converts D-serine to pyruvate and ammonium.
- D-serine-transport:
- cycA
- or dsdX
- Comment: Transporters were identified using query: transporter:D-serine:D-ser
Steps
cycA: D-serine:H+ symporter CycA
- Curated sequence A0A0H2VDI7: D-serine/D-alanine/glycine transporter
- Curated sequence P0AAE0: D-serine/D-alanine/glycine transporter. D-Serine/D-alanine/glycine/D-cycloserine:H+ symporter. D-serine/alanine/glycine/:H+symporter. D-serine/alanine/glycine/:H+symporter
- Curated sequence F2HQ24: Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21)
- Curated sequence M1IW84: D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA
- Curated sequence A2RI86: DL-alanine permease SerP2
- Total: 5 characterized proteins
dsdX: D-serine transporter DsdX
- Curated sequence A0A0H2VAP9: D-serine transporter DsdX; D-serine-specific permease
- Curated sequence P08555: D-serine transporter DsdX. The D-serine transporter, DsdX (KM=60µM) (may also transport D-threonine which inhibits D-serine uptake) (Anfora and Welch, 2006). Eliminating the dsdX gene renders the cell more sensitive to chloramphenicol. D-serine transporter
- Total: 2 characterized proteins
dsdA: D-serine ammonia-lyase
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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:
- 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, 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