GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Sinorhizobium meliloti 1021

Best path

gguA, gguB, chvE, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA SM_b20894 SM_b20713
gguB L-arabinose ABC transporter, permease component GguB SM_b20893 SMc02031
chvE L-arabinose ABC transporter, substrate-binding component ChvE SM_b20895
xacB L-arabinose 1-dehydrogenase SMc00588 SM_b20511
xacC L-arabinono-1,4-lactonase SMc00883 SMa0717
xacD L-arabinonate dehydratase SM_b20890 SMc00884
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase SM_b20892
xacF alpha-ketoglutarate semialdehyde dehydrogenase SM_b20891 SM_b20262
Alternative steps:
aldA (glycol)aldehyde dehydrogenase SMc02780 SM_b21185
aldox-large (glycol)aldehyde oxidoreductase, large subunit SMc03102 SM_b20132
aldox-med (glycol)aldehyde oxidoreductase, medium subunit SMc03103 SM_b20130
aldox-small (glycol)aldehyde oxidoreductase, small subunit SMc03101 SM_b20131
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF SM_b20508
araG L-arabinose ABC transporter, ATPase component AraG SM_b20507 SMc02337
araH L-arabinose ABC transporter, permease component AraH SM_b20506 SM_b21375
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) SM_b20632
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) SM_b21587 SM_b21345
araV L-arabinose ABC transporter, ATPase component AraV SM_b20235 SMc03065
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) SM_b21588 SM_b21344
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) SM_b21589 SM_b21343
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) SM_b21590 SM_b21342
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase SMc02581
gyaR glyoxylate reductase SMc02849 SMc01943
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) SMc04395 SMa1339
xacI L-arabinose ABC transporter, permease component 2 (XacI) SMc04394
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) SM_b20972 SM_b20661
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) SM_b20419 SMc02474
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG SMa0216 SMc03815
xylHsa L-arabinose ABC transporter, permease component XylH SMc02019 SMa0070

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