GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Brucella inopinata BO1

Best path

gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA BIBO1_RS18905 BIBO1_RS15355
gguB L-arabinose ABC transporter, permease component GguB BIBO1_RS18900 BIBO1_RS15360
chvE L-arabinose ABC transporter, substrate-binding component ChvE BIBO1_RS18910 BIBO1_RS15350
xacB L-arabinose 1-dehydrogenase BIBO1_RS18930 BIBO1_RS08590
xacC L-arabinono-1,4-lactonase BIBO1_RS0103155
xacD L-arabinonate dehydratase BIBO1_RS18925 BIBO1_RS10395
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase BIBO1_RS18935
xacF alpha-ketoglutarate semialdehyde dehydrogenase BIBO1_RS10860 BIBO1_RS11605
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BIBO1_RS11605 BIBO1_RS17145
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BIBO1_RS13270
aldox-small (glycol)aldehyde oxidoreductase, small subunit BIBO1_RS13270
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG BIBO1_RS15355 BIBO1_RS11590
araH L-arabinose ABC transporter, permease component AraH BIBO1_RS19485 BIBO1_RS11585
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 BIBO1_RS16280 BIBO1_RS16955
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) BIBO1_RS19475 BIBO1_RS11590
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) BIBO1_RS14065 BIBO1_RS11585
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) BIBO1_RS11585 BIBO1_RS18545
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase BIBO1_RS11635 BIBO1_RS18635
gyaR glyoxylate reductase BIBO1_RS06720 BIBO1_RS11805
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)
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) BIBO1_RS17945 BIBO1_RS16720
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BIBO1_RS12775 BIBO1_RS16720
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG BIBO1_RS09800 BIBO1_RS19475
xylHsa L-arabinose ABC transporter, permease component XylH BIBO1_RS11585

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 24 2021. The underlying query database was built on Sep 17 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 (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