GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Pseudomonas fluorescens FW300-N1B4

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF Pf1N1B4_411
araG L-arabinose ABC transporter, ATPase component AraG Pf1N1B4_410 Pf1N1B4_4286
araH L-arabinose ABC transporter, permease component AraH Pf1N1B4_409 Pf1N1B4_4287
xacB L-arabinose 1-dehydrogenase Pf1N1B4_412 Pf1N1B4_512
xacC L-arabinono-1,4-lactonase Pf1N1B4_413 Pf1N1B4_4510
xacD L-arabinonate dehydratase Pf1N1B4_4621 Pf1N1B4_398
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase Pf1N1B4_4623 Pf1N1B4_3384
xacF alpha-ketoglutarate semialdehyde dehydrogenase Pf1N1B4_1109 Pf1N1B4_4624
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Pf1N1B4_5695 Pf1N1B4_4931
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Pf1N1B4_4870 Pf1N1B4_4583
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)
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) Pf1N1B4_4285
araV L-arabinose ABC transporter, ATPase component AraV Pf1N1B4_3974 Pf1N1B4_4847
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) Pf1N1B4_4286 Pf1N1B4_410
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) Pf1N1B4_4287 Pf1N1B4_6033
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) Pf1N1B4_4287 Pf1N1B4_6033
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 Pf1N1B4_4286 Pf1N1B4_6034
gguB L-arabinose ABC transporter, permease component GguB
glcB malate synthase Pf1N1B4_2478
gyaR glyoxylate reductase Pf1N1B4_1004 Pf1N1B4_4763
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) Pf1N1B4_595
xacI L-arabinose ABC transporter, permease component 2 (XacI) Pf1N1B4_594
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) Pf1N1B4_593 Pf1N1B4_4847
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) Pf1N1B4_593 Pf1N1B4_4847
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG Pf1N1B4_4286 Pf1N1B4_1724
xylHsa L-arabinose ABC transporter, permease component XylH Pf1N1B4_4287

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 Aug 02 2021. The underlying query database was built on Aug 02 2021.

Links

Downloads

Related tools

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, 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