L-arabinose catabolism in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

L-arabinose catabolism in Dinoroseobacter shibae DFL-12

Best path

Also see fitness data for the top candidates

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
araE	L-arabinose:H+ symporter
xacB	L-arabinose 1-dehydrogenase	Dshi_1243	Dshi_1358
xacC	L-arabinono-1,4-lactonase	Dshi_1240
xacD	L-arabinonate dehydratase	Dshi_1244	Dshi_0129
xacE	2-dehydro-3-deoxy-L-arabinonate dehydratase	Dshi_2446
xacF	alpha-ketoglutarate semialdehyde dehydrogenase	Dshi_0577	Dshi_2442
Alternative steps:
aldA	(glycol)aldehyde dehydrogenase	Dshi_2887	Dshi_1425
aldox-large	(glycol)aldehyde oxidoreductase, large subunit	Dshi_2659	Dshi_4202
aldox-med	(glycol)aldehyde oxidoreductase, medium subunit	Dshi_1210	Dshi_4200
aldox-small	(glycol)aldehyde oxidoreductase, small subunit	Dshi_1211	Dshi_2660
araA	L-arabinose isomerase
araB	ribulokinase	Dshi_0537
araD	L-ribulose-5-phosphate epimerase
araF	L-arabinose ABC transporter, substrate-binding component AraF
araG	L-arabinose ABC transporter, ATPase component AraG	Dshi_2433	Dshi_0530
araH	L-arabinose ABC transporter, permease component AraH	Dshi_2431	Dshi_2432
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)
araV	L-arabinose ABC transporter, ATPase component AraV	Dshi_2017	Dshi_3141
araVsh	L-arabinose ABC transporter, ATPase component AraV(Sh)	Dshi_2433	Dshi_0530
araWsh	L-arabinose ABC transporter, permease component 1 AraW(Sh)	Dshi_0528
araZsh	L-arabinose ABC transporter, permease component 2 AraZ(Sh)	Dshi_2432	Dshi_0389
BT0355	L-arabinose:Na+ symporter	Dshi_3906	Dshi_3904
chvE	L-arabinose ABC transporter, substrate-binding component ChvE
Echvi_1880	L-arabinose:Na+ symporter	Dshi_3906	Dshi_3904
gguA	L-arabinose ABC transporter, ATPase component GguA	Dshi_2433	Dshi_0530
gguB	L-arabinose ABC transporter, permease component GguB	Dshi_1999
glcB	malate synthase	Dshi_1227	Dshi_2874
gyaR	glyoxylate reductase	Dshi_2970	Dshi_2643
KDG-aldolase	2-dehydro-3-deoxy-L-arabinonate aldolase
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)	Dshi_3141	Dshi_1416
xacK	L-arabinose ABC transporter, ATPase component 2 (XacK)	Dshi_0546	Dshi_1416
xylFsa	L-arabinose ABC transporter, substrate-binding component XylF
xylGsa	L-arabinose ABC transporter, ATPase component XylG	Dshi_1998	Dshi_1276
xylHsa	L-arabinose ABC transporter, permease component XylH

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 17 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