GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Dyella japonica UNC79MFTsu3.2

Best path

araUsh, araVsh, araWsh, araZsh, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) N515DRAFT_2412
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) N515DRAFT_2413 N515DRAFT_3232
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) N515DRAFT_2414 N515DRAFT_2415
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) N515DRAFT_2415 N515DRAFT_2414
xacB L-arabinose 1-dehydrogenase N515DRAFT_1230 N515DRAFT_1253
xacC L-arabinono-1,4-lactonase N515DRAFT_1229
xacD L-arabinonate dehydratase N515DRAFT_2409 N515DRAFT_0569
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase N515DRAFT_2411
xacF alpha-ketoglutarate semialdehyde dehydrogenase N515DRAFT_0954 N515DRAFT_3729
Alternative steps:
aldA (glycol)aldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_2488
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit N515DRAFT_2295 N515DRAFT_4010
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter N515DRAFT_1228 N515DRAFT_0382
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG N515DRAFT_3232 N515DRAFT_2413
araH L-arabinose ABC transporter, permease component AraH
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)
araV L-arabinose ABC transporter, ATPase component AraV N515DRAFT_4212 N515DRAFT_1562
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE N515DRAFT_3231
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA N515DRAFT_3232 N515DRAFT_2413
gguB L-arabinose ABC transporter, permease component GguB N515DRAFT_3233
glcB malate synthase N515DRAFT_4124
gyaR glyoxylate reductase N515DRAFT_0108 N515DRAFT_3581
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) N515DRAFT_3134
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) N515DRAFT_4212 N515DRAFT_1562
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) N515DRAFT_4212 N515DRAFT_1562
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG N515DRAFT_2413 N515DRAFT_3232
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 (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:

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. 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:

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 preprint 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