GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Bacteroides thetaiotaomicron VPI-5482

Best path

BT0355, araA, araB, araD

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BT0355 L-arabinose:Na+ symporter BT0355 BT0341
araA L-arabinose isomerase BT0351
araB ribulokinase BT0350
araD L-ribulose-5-phosphate epimerase BT0353
Alternative steps:
aldA (glycol)aldehyde dehydrogenase
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit
araE L-arabinose:H+ symporter BT0436 BT4397
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG
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)
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh)
araV L-arabinose ABC transporter, ATPase component AraV BT1291 BT1751
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh)
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh)
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
chvE L-arabinose ABC transporter, substrate-binding component ChvE
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA
gguB L-arabinose ABC transporter, permease component GguB
glcB malate synthase
gyaR glyoxylate reductase BT1207 BT1575
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase BT3771 BT1015
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase BT2078
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase
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) BT1291 BT1751
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BT1291 BT1751
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG BT1291 BT0509
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.

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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, 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