GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Pseudomonas fluorescens FW300-N2E3

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter
xacB L-arabinose 1-dehydrogenase AO353_00945 AO353_01660
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase AO353_03420 AO353_08345
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase AO353_05300 AO353_14870
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AO353_28230 AO353_11505
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit AO353_23430 AO353_01425
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 AO353_21385 AO353_20820
araH L-arabinose ABC transporter, permease component AraH AO353_21390
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) AO353_21380
araV L-arabinose ABC transporter, ATPase component AraV AO353_25895 AO353_03380
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) AO353_21385 AO353_20820
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) AO353_21390 AO353_20825
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
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 AO353_21385 AO353_20820
gguB L-arabinose ABC transporter, permease component GguB
glcB malate synthase AO353_07560
gyaR glyoxylate reductase AO353_04850 AO353_26885
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) AO353_03390
xacI L-arabinose ABC transporter, permease component 2 (XacI) AO353_03385
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) AO353_03380 AO353_25895
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) AO353_03380 AO353_25895
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG AO353_21385 AO353_11555
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 Apr 09 2024. 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:

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