GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Escherichia coli BW25113

Best path

araF, araG, araH, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF b1901
araG L-arabinose ABC transporter, ATPase component AraG b1900 b3749
araH L-arabinose ABC transporter, permease component AraH b4460 b2546
araA L-arabinose isomerase b0062
araB ribulokinase b0063
araD L-ribulose-5-phosphate epimerase b3583 b0061
Alternative steps:
aldA (glycol)aldehyde dehydrogenase b1415 b2661
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit b0286 b2868
araE L-arabinose:H+ symporter b2841 b2943
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) b4227 b3751
araV L-arabinose ABC transporter, ATPase component AraV b0262 b3450
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) b4485 b3749
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) b4230 b3750
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) b4231 b3750
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE b3566
Echvi_1880 L-arabinose:Na+ symporter b3679
gguA L-arabinose ABC transporter, ATPase component GguA b3567 b3749
gguB L-arabinose ABC transporter, permease component GguB b3568 b3750
glcB malate synthase b2976 b4014
gyaR glyoxylate reductase b3553 b2913
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase b2426 b1619
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase b3771 b1851
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase b2661 b0312
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH) b3452
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) b4035 b3450
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) b3450 b4035
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG b3749 b4485
xylHsa L-arabinose ABC transporter, permease component XylH b3750 b2546

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