GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Caulobacter crescentus NA1000

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter CCNA_00857
xacB L-arabinose 1-dehydrogenase CCNA_01018 CCNA_00864
xacC L-arabinono-1,4-lactonase CCNA_00863 CCNA_01882
xacD L-arabinonate dehydratase CCNA_01488 CCNA_00862
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase CCNA_01486
xacF alpha-ketoglutarate semialdehyde dehydrogenase CCNA_00865 CCNA_02881
Alternative steps:
aldA (glycol)aldehyde dehydrogenase CCNA_03242 CCNA_00424
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit CCNA_00022 CCNA_02353
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG CCNA_00903
araH L-arabinose ABC transporter, permease component AraH CCNA_00904
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 CCNA_03235 CCNA_01670
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) CCNA_00903
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) CCNA_00904
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) CCNA_00904
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA CCNA_00903
gguB L-arabinose ABC transporter, permease component GguB CCNA_00904
glcB malate synthase CCNA_01843
gyaR glyoxylate reductase CCNA_03838 CCNA_03322
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) CCNA_03235 CCNA_01670
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) CCNA_03235 CCNA_01670
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG CCNA_00903 CCNA_00366
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