L-aspartate catabolism in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

L-aspartate catabolism in Halomonas desiderata SP1

Best path

Rules

Overview: Aspartate can be transaminated to oxaloacetate, which is an intermediate in central metabolism, so GapMind only represents uptake.

all: aspartate-transport
aspartate-transport:

bztA, bztB, bztC and bztD
or peb1A, peb1B, peb1C and peb1D
or aatJ, aatQ, aatM and aatP
or natF, bgtB', natH and bgtA
or natF, natG, natH and bgtA
or aapJ, aapQ, aapM and aapP
or glt
or acaP
or SLC7A13
or BPHYT_RS17540
or yveA
or dauA
Comment: To find transporters, used query: transporter:aspartate:L-aspartate

27 steps (20 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
dauA	dicarboxylic acid transporter DauA	BZY95_RS11745	BZY95_RS20600
Alternative steps:
aapJ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ	BZY95_RS06440
aapM	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)	BZY95_RS06450	BZY95_RS12915
aapP	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP	BZY95_RS02565	BZY95_RS12910
aapQ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)	BZY95_RS06445
aatJ	aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM	aspartate/asparagine ABC transporter, permease component 2 (AatM)	BZY95_RS06450	BZY95_RS12915
aatP	aspartate/asparagine ABC transporter, ATPase component	BZY95_RS02565	BZY95_RS12910
aatQ	aspartate/asparagine ABC transporter, permease component 1 (AatQ)	BZY95_RS06445
acaP	aspartate permease AcaP
bgtA	aspartate ABC transporter, ATPase component BgtA	BZY95_RS02565	BZY95_RS12910
bgtB'	aspartate ABC transporter, permease component 1 (BgtB)	BZY95_RS06445
BPHYT_RS17540	aspartate:H+ (or asparagine) symporter
bztA	aspartate/asparagine ABC transporter, substrate-binding component BztA	BZY95_RS06440
bztB	aspartate/asparagine ABC transporter, permease component 1 (BztB)	BZY95_RS06445
bztC	aspartate/asparagine ABC transporter, permease component 2 (BztC)	BZY95_RS06450
bztD	aspartate/asparagine ABC transporter, ATPase component (BztD)	BZY95_RS02565	BZY95_RS12910
glt	aspartate:proton symporter Glt
natF	aspartate ABC transporter, substrate-binding component NatF	BZY95_RS06440
natG	aspartate ABC transporter, permease component 1 (NatG)	BZY95_RS06445	BZY95_RS02560
natH	aspartate ABC transporter, permease component 2 (NatH)	BZY95_RS06450	BZY95_RS02050
peb1A	aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B	aspartate ABC transporter, permease component 1 (Peb1B)	BZY95_RS06445
peb1C	aspartate ABC transporter, ATPase component Peb1C	BZY95_RS02565	BZY95_RS12910
peb1D	aspartate ABC transporter, permease component 2 (Peb1D)	BZY95_RS06450
SLC7A13	sodium-independent aspartate transporter
yveA	aspartate:proton symporter YveA

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