GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Pseudomonas fluorescens FW300-N2E2

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF Pf6N2E2_5968
araG L-arabinose ABC transporter, ATPase component AraG Pf6N2E2_5969 Pf6N2E2_523
araH L-arabinose ABC transporter, permease component AraH Pf6N2E2_5970 Pf6N2E2_524
xacB L-arabinose 1-dehydrogenase Pf6N2E2_5967 Pf6N2E2_1441
xacC L-arabinono-1,4-lactonase Pf6N2E2_5966 Pf6N2E2_488
xacD L-arabinonate dehydratase Pf6N2E2_609 Pf6N2E2_1668
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase Pf6N2E2_611 Pf6N2E2_3203
xacF alpha-ketoglutarate semialdehyde dehydrogenase Pf6N2E2_612 Pf6N2E2_3298
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Pf6N2E2_1102 Pf6N2E2_1751
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit Pf6N2E2_1203 Pf6N2E2_5938
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter Pf6N2E2_883
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) Pf6N2E2_522 Pf6N2E2_1005
araV L-arabinose ABC transporter, ATPase component AraV Pf6N2E2_1960 Pf6N2E2_807
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) Pf6N2E2_523 Pf6N2E2_5969
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) Pf6N2E2_524
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE Pf6N2E2_1455
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA Pf6N2E2_1456 Pf6N2E2_523
gguB L-arabinose ABC transporter, permease component GguB Pf6N2E2_1457
glcB malate synthase Pf6N2E2_4752
gyaR glyoxylate reductase Pf6N2E2_5310 Pf6N2E2_627
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) Pf6N2E2_2891
xacI L-arabinose ABC transporter, permease component 2 (XacI) Pf6N2E2_2890
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) Pf6N2E2_2889 Pf6N2E2_807
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) Pf6N2E2_807 Pf6N2E2_2889
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG Pf6N2E2_523 Pf6N2E2_1456
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 (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 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