GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Cupriavidus basilensis 4G11

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter
xacB L-arabinose 1-dehydrogenase RR42_RS30145 RR42_RS25125
xacC L-arabinono-1,4-lactonase RR42_RS30140 RR42_RS33665
xacD L-arabinonate dehydratase RR42_RS33950 RR42_RS18585
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase RR42_RS23085
xacF alpha-ketoglutarate semialdehyde dehydrogenase RR42_RS23090 RR42_RS04830
Alternative steps:
aldA (glycol)aldehyde dehydrogenase RR42_RS11330 RR42_RS21760
aldox-large (glycol)aldehyde oxidoreductase, large subunit RR42_RS02365 RR42_RS26495
aldox-med (glycol)aldehyde oxidoreductase, medium subunit RR42_RS13625 RR42_RS26500
aldox-small (glycol)aldehyde oxidoreductase, small subunit RR42_RS02370 RR42_RS13620
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 RR42_RS32900 RR42_RS03360
araH L-arabinose ABC transporter, permease component AraH RR42_RS03365 RR42_RS32890
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 RR42_RS18590 RR42_RS22875
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) RR42_RS32900 RR42_RS03360
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) RR42_RS03365 RR42_RS32895
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) RR42_RS03365 RR42_RS32895
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 RR42_RS32900 RR42_RS03360
gguB L-arabinose ABC transporter, permease component GguB RR42_RS03365
glcB malate synthase RR42_RS12175 RR42_RS24325
gyaR glyoxylate reductase RR42_RS14190 RR42_RS33330
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) RR42_RS18590 RR42_RS22875
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) RR42_RS18590 RR42_RS12955
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG RR42_RS32900 RR42_RS03360
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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