L-arabinose catabolism in Dyadobacter tibetensis Y620-1

GapMind for catabolism of small carbon sources

L-arabinose catabolism in Dyadobacter tibetensis Y620-1

Best path

Rules

Overview: L-arabinose utilization in GapMind is based on MetaCyc pathways L-arabinose degradation I, via xylulose 5-phosphate (link); III, oxidation to 2-oxoglutarate (link); and IV, via glycolaldehyde (link). Pathway II via xylitol and xylulose is not represented in GapMind because it is not reported in prokaryotes (link).

glycolaldehyde-dehydrogenase:

aldA
or aldox-large, aldox-med and aldox-small

all:

arabinose-transport, araA, araB and araD
or arabinose-transport, xacB, xacC, xacD, xacE and xacF
or arabinose-transport, xacB, xacC, xacD, KDG-aldolase, glycolaldehyde-dehydrogenase, gyaR and glcB
Comment: In pathway I, isomerase araA forms L-ribulose, kinase araB forms ribulose 5-phosphate, and epimerase araD forms D-xylulose 5-phosphate, which is an intermediate in the pentose phosphate pathway. In pathway III, the 1-dehydrogenase xacB (which acts on the furanose form, not the usual pyranose form?) forms arabino-1,4-lactone, lactonase xacC forms arbinonate, two dehydratases form 2-dehydro-3-deoxy-L-arabinonate and 2,5-dioxopentanonate (α-ketoglutarate semialdehyde), and dehydrogenase xacF forms 2-oxoglutarate, which is an intermediate in the TCA cycle. (Fitness data suggests that L-arabinose 1-epimerase or mutarotase is also involved, perhaps in creating the correct epimer for the 1-dehydrogenase, but is not included in GapMind.) Pathway IV begins as in pathway III, to 2-dehydro-3-deoxy-L-arabinonate, followed by KDG aldolase to pyruvate and glycolaldehyde; the glycolaldehyde is oxidized to glycolate and then to glyoxylate, and combined with acetyl-CoA by malate synthase, which is a TCA cycle intermediate. (Other pathways for glyxoylate assimilation are known but are not represented here.)

arabinose-transport:

gguA, gguB and chvE
or araF, araG and araH
or araS, araT, araU and araV
or xacG, xacH, xacI, xacJ and xacK
or xylFsa, xylGsa and xylHsa
or araUsh, araVsh, araWsh and araZsh
or araE
or BT0355
or Echvi_1880
Comment: Transporters were identified using query: transporter:arabinose:L-arabinose:L-arabinofuranose:L-arabinopyranose:beta-L-arabinose:CPD-12045:CPD-12046

40 steps (25 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
Echvi_1880	L-arabinose:Na+ symporter	X939_RS0104810	X939_RS0110740
araA	L-arabinose isomerase	X939_RS0104435
araB	ribulokinase	X939_RS0117400	X939_RS0104430
araD	L-ribulose-5-phosphate epimerase	X939_RS0117395
Alternative steps:
aldA	(glycol)aldehyde dehydrogenase	X939_RS0100145	X939_RS0103685
aldox-large	(glycol)aldehyde oxidoreductase, large subunit
aldox-med	(glycol)aldehyde oxidoreductase, medium subunit
aldox-small	(glycol)aldehyde oxidoreductase, small subunit	X939_RS0109420	X939_RS0102820
araE	L-arabinose:H+ symporter	X939_RS0108280
araF	L-arabinose ABC transporter, substrate-binding component AraF
araG	L-arabinose ABC transporter, ATPase component AraG	X939_RS0116940	X939_RS0121525
araH	L-arabinose ABC transporter, permease component AraH	X939_RS0121530	X939_RS0116935
araS	L-arabinose ABC transporter, substrate-binding component AraS
araT	L-arabinose ABC transporter, permease component 1 (AraT)
araU	L-arabinose ABC transporter, permease component 2 (AraU)
araUsh	L-arabinose ABC transporter, substrate-binding component AraU(Sh)	X939_RS0110160
araV	L-arabinose ABC transporter, ATPase component AraV	X939_RS0112600	X939_RS0117935
araVsh	L-arabinose ABC transporter, ATPase component AraV(Sh)	X939_RS0121525	X939_RS0116940
araWsh	L-arabinose ABC transporter, permease component 1 AraW(Sh)	X939_RS0116935	X939_RS0121530
araZsh	L-arabinose ABC transporter, permease component 2 AraZ(Sh)	X939_RS0121530	X939_RS0116935
BT0355	L-arabinose:Na+ symporter	X939_RS0110740	X939_RS0104810
chvE	L-arabinose ABC transporter, substrate-binding component ChvE
gguA	L-arabinose ABC transporter, ATPase component GguA	X939_RS0116940	X939_RS0121525
gguB	L-arabinose ABC transporter, permease component GguB	X939_RS0116935
glcB	malate synthase
gyaR	glyoxylate reductase	X939_RS0109265	X939_RS0102530
KDG-aldolase	2-dehydro-3-deoxy-L-arabinonate aldolase
xacB	L-arabinose 1-dehydrogenase	X939_RS0111250	X939_RS0111485
xacC	L-arabinono-1,4-lactonase
xacD	L-arabinonate dehydratase	X939_RS0110295	X939_RS0114785
xacE	2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF	alpha-ketoglutarate semialdehyde dehydrogenase	X939_RS0109240	X939_RS0100145
xacG	L-arabinose ABC transporter, substrate-binding component XacG
xacH	L-arabinose ABC transporter, permease component 1 (XacH)
xacI	L-arabinose ABC transporter, permease component 2 (XacI)
xacJ	L-arabinose ABC transporter, ATPase component 1 (XacJ)	X939_RS0117935	X939_RS0112600
xacK	L-arabinose ABC transporter, ATPase component 2 (XacK)	X939_RS0117935	X939_RS0112600
xylFsa	L-arabinose ABC transporter, substrate-binding component XylF
xylGsa	L-arabinose ABC transporter, ATPase component XylG	X939_RS0121525	X939_RS0116940
xylHsa	L-arabinose ABC transporter, permease component XylH	X939_RS0121530

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