GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Dinoroseobacter shibae DFL-12

Best path

araE, xacB, xacC, xacD, xacE, xacF

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).

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.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, 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