GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

Echvi_1880, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Echvi_1880 L-arabinose:Na+ symporter Echvi_1880 Echvi_1871
araA L-arabinose isomerase Echvi_1879
araB ribulokinase Echvi_0515 Echvi_4514
araD L-ribulose-5-phosphate epimerase Echvi_0503
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Echvi_0481 Echvi_3822
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Echvi_4165
araE L-arabinose:H+ symporter Echvi_2805 Echvi_2810
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG Echvi_1282
araH L-arabinose ABC transporter, permease component AraH Echvi_1280
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 Echvi_1022 Echvi_3653
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) Echvi_1282
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) Echvi_1280
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) Echvi_1280
BT0355 L-arabinose:Na+ symporter Echvi_1680 Echvi_1871
chvE L-arabinose ABC transporter, substrate-binding component ChvE
gguA L-arabinose ABC transporter, ATPase component GguA Echvi_1282
gguB L-arabinose ABC transporter, permease component GguB Echvi_1280
glcB malate synthase
gyaR glyoxylate reductase Echvi_3936 Echvi_2777
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase Echvi_2940 Echvi_3364
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase Echvi_2055 Echvi_3769
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase Echvi_3952 Echvi_0481
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) Echvi_2123 Echvi_1022
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) Echvi_2123 Echvi_3653
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG Echvi_1282 Echvi_1333
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