GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Pseudomonas simiae WCS417

Best path

araF, araG, araH, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF PS417_21335 PS417_11025
araG L-arabinose ABC transporter, ATPase component AraG PS417_21330 PS417_11030
araH L-arabinose ABC transporter, permease component AraH PS417_21325 PS417_11035
xacB L-arabinose 1-dehydrogenase PS417_21340 PS417_11045
xacC L-arabinono-1,4-lactonase PS417_11020 PS417_07255
xacD L-arabinonate dehydratase PS417_11000 PS417_22690
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase PS417_11010 PS417_06885
xacF alpha-ketoglutarate semialdehyde dehydrogenase PS417_11015 PS417_04200
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PS417_00895 PS417_05945
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit PS417_24365
aldox-small (glycol)aldehyde oxidoreductase, small subunit PS417_24370 PS417_13030
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
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) PS417_22135
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh)
araV L-arabinose ABC transporter, ATPase component AraV PS417_12700 PS417_22130
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) PS417_11890 PS417_17730
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) PS417_12060 PS417_11895
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) PS417_12060 PS417_17725
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE PS417_10940
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA PS417_10935 PS417_11890
gguB L-arabinose ABC transporter, permease component GguB PS417_10930 PS417_12060
glcB malate synthase PS417_26040
gyaR glyoxylate reductase PS417_04730 PS417_12555
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) PS417_22140
xacI L-arabinose ABC transporter, permease component 2 (XacI) PS417_22135
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) PS417_22130 PS417_12700
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) PS417_22130 PS417_12700
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG PS417_17730 PS417_11890
xylHsa L-arabinose ABC transporter, permease component XylH PS417_11895

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