GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Burkholderia phytofirmans PsJN

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF BPHYT_RS16935 BPHYT_RS19715
araG L-arabinose ABC transporter, ATPase component AraG BPHYT_RS16930 BPHYT_RS19720
araH L-arabinose ABC transporter, permease component AraH BPHYT_RS16925 BPHYT_RS19725
xacB L-arabinose 1-dehydrogenase BPHYT_RS16920 BPHYT_RS16940
xacC L-arabinono-1,4-lactonase BPHYT_RS16915 BPHYT_RS24170
xacD L-arabinonate dehydratase BPHYT_RS19730 BPHYT_RS21270
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase BPHYT_RS22715
xacF alpha-ketoglutarate semialdehyde dehydrogenase BPHYT_RS10925 BPHYT_RS28455
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BPHYT_RS09875 BPHYT_RS34305
aldox-large (glycol)aldehyde oxidoreductase, large subunit BPHYT_RS01765
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BPHYT_RS10830 BPHYT_RS01760
aldox-small (glycol)aldehyde oxidoreductase, small subunit BPHYT_RS01770 BPHYT_RS10825
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) BPHYT_RS23870 BPHYT_RS01825
araV L-arabinose ABC transporter, ATPase component AraV BPHYT_RS32360 BPHYT_RS09400
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) BPHYT_RS01820 BPHYT_RS23875
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) BPHYT_RS23880 BPHYT_RS01815
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) BPHYT_RS23885 BPHYT_RS01810
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE BPHYT_RS32820
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA BPHYT_RS32815 BPHYT_RS27185
gguB L-arabinose ABC transporter, permease component GguB BPHYT_RS32810 BPHYT_RS27190
glcB malate synthase BPHYT_RS31665 BPHYT_RS09815
gyaR glyoxylate reductase BPHYT_RS14520 BPHYT_RS20960
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) BPHYT_RS05030
xacI L-arabinose ABC transporter, permease component 2 (XacI) BPHYT_RS05035
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) BPHYT_RS35680 BPHYT_RS05040
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BPHYT_RS35680 BPHYT_RS05040
xylFsa L-arabinose ABC transporter, substrate-binding component XylF BPHYT_RS30855
xylGsa L-arabinose ABC transporter, ATPase component XylG BPHYT_RS30865 BPHYT_RS22735
xylHsa L-arabinose ABC transporter, permease component XylH BPHYT_RS30860 BPHYT_RS25825

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