GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Shewanella sp. ANA-3

Best path

araUsh, araVsh, araWsh, araZsh, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) Shewana3_2073
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) Shewana3_2074
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) Shewana3_2075
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) Shewana3_2076
araA L-arabinose isomerase Shewana3_2066
araB ribulokinase Shewana3_2064
araD L-ribulose-5-phosphate epimerase Shewana3_2065
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Shewana3_3092 Shewana3_0250
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Shewana3_1496
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG Shewana3_2074
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 Shewana3_3096 Shewana3_3192
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 Shewana3_2074
gguB L-arabinose ABC transporter, permease component GguB Shewana3_2076
glcB malate synthase Shewana3_2943
gyaR glyoxylate reductase Shewana3_3416 Shewana3_3319
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase Shewana3_2071 Shewana3_2690
xacC L-arabinono-1,4-lactonase Shewana3_2088
xacD L-arabinonate dehydratase Shewana3_2070 Shewana3_2149
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase Shewana3_3092 Shewana3_3105
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) Shewana3_3096 Shewana3_3192
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) Shewana3_3192 Shewana3_3096
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG Shewana3_2074 Shewana3_0880
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