Definition of D-alanine catabolism
As rules and steps, or see full text
Rules
Overview: GapMind describes D-alanine catabolism via D-alanine dehydrogenase, which forms pyruvate. This reaction is part of the MetaCyc pathway for L-alanine catabolism via D-alanine (link). In principle, D-alanine might also be catabolized via racemization to L-alanine and transamination to pyruvate, but this is not described here.
- all: D-alanine-transport and dadA
- D-alanine-transport:
Steps
Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component
Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2
Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1
Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component
AZOBR_RS08235: D-alanine ABC transporter, permease component 1
- Curated sequence AZOBR_RS08235: L-proline and D-alanine ABC transporter, permease component 1
- Comment: An ABC transporter from Azospirillum brasilense, with 5 components, was identified in the fitness data. (Just one component was in the reannotations.) MctP was missed by the clustering tool, but is annotated as transporting D-alanine (see PMC135354, Figure 4A, showing that D-alanine inhibits transport). A related protein, BPHYT_RS22245 (B2T7V3), is involved in D-alanine utilization.
- Total: 1 characterized proteins
AZOBR_RS08240: D-alanine ABC transporter, permease component 2
- UniProt sequence G8ALI9: SubName: Full=Leucine/isoleucine/valine ABC transporter,permease component {ECO:0000313|EMBL:CCC98101.1};
- Total: 1 characterized proteins
AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1
- UniProt sequence G8ALJ0: SubName: Full=Leucine/isoleucine/valine ABC transporter,ATPase component {ECO:0000313|EMBL:CCC98102.1}; EC=3.6.3.- {ECO:0000313|EMBL:CCC98102.1};
- Total: 1 characterized proteins
AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2
- UniProt sequence G8ALJ1: SubName: Full=Leucine//isoleucine/valine ABC transporter,ATPase component {ECO:0000313|EMBL:CCC98103.1}; EC=3.6.3.- {ECO:0000313|EMBL:CCC98103.1};
- Total: 1 characterized proteins
AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component
- UniProt sequence G8ALJ3: SubName: Full=Branched-chain amino acid ABC transporter,substrate-binding periplasmic component {ECO:0000313|EMBL:CCC98105.1};
- Total: 1 characterized proteins
cycA: D-alanine: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 GFF1065: L-alanine and D-alanine permease
- Curated sequence AO353_16120: D-alanine and L-alanine transporter
- Curated sequence AO356_17670: L-alanine and D-alanine permease
- Curated sequence A2RI86: DL-alanine permease SerP2
- Total: 8 characterized proteins
mctP: D-alanine transporter MctP
- Curated sequence Q8VM88: The monocarboxylate uptake (H+ symport?) permease, MctP (transports lactate (Km = 4.4 μM), pyruvate (Km = 3.8), propionate, butyrate (butanoic acid), α-hydroxybutyrate, L- and D-alanine (Km = 0.5 mM), and possibly cysteine and histidine)
- Curated sequence Q1M7A2: Monocarboxylate transport permease protein
- UniProt sequence B2T7V3: SubName: Full=Na+/solute symporter {ECO:0000313|EMBL:ACD18855.1};
- Total: 3 characterized proteins
dadA: D-alanine dehydrogenase
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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