GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Pseudomonas fluorescens FW300-N2C3

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF AO356_20245
araG L-arabinose ABC transporter, ATPase component AraG AO356_20250 AO356_23205
araH L-arabinose ABC transporter, permease component AraH AO356_20255 AO356_23210
xacB L-arabinose 1-dehydrogenase AO356_20240 AO356_28440
xacC L-arabinono-1,4-lactonase AO356_20235 AO356_23060
xacD L-arabinonate dehydratase AO356_24585 AO356_28760
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase AO356_24595 AO356_06755
xacF alpha-ketoglutarate semialdehyde dehydrogenase AO356_24600 AO356_07180
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AO356_26145 AO356_26740
aldox-large (glycol)aldehyde oxidoreductase, large subunit AO356_26665
aldox-med (glycol)aldehyde oxidoreductase, medium subunit AO356_26660 AO356_15625
aldox-small (glycol)aldehyde oxidoreductase, small subunit AO356_26655 AO356_15620
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter AO356_27270
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 AO356_00010 AO356_01640
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) AO356_23205 AO356_20250
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) AO356_23210
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE AO356_28505
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA AO356_28510 AO356_23205
gguB L-arabinose ABC transporter, permease component GguB AO356_28515
glcB malate synthase AO356_14100
gyaR glyoxylate reductase AO356_16925 AO356_24675
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) AO356_05190
xacI L-arabinose ABC transporter, permease component 2 (XacI) AO356_05185
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) AO356_05180 AO356_27685
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) AO356_05180 AO356_27685
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG AO356_23205 AO356_28510
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