GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Duganella sacchari Sac-22

Best path

araE, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter BUA36_RS18045
xacB L-arabinose 1-dehydrogenase BUA36_RS25685 BUA36_RS22870
xacC L-arabinono-1,4-lactonase BUA36_RS22905 BUA36_RS13650
xacD L-arabinonate dehydratase BUA36_RS22810 BUA36_RS22860
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase BUA36_RS17085 BUA36_RS13655
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BUA36_RS07090 BUA36_RS13005
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit BUA36_RS16595 BUA36_RS19880
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 BUA36_RS11790 BUA36_RS13070
araH L-arabinose ABC transporter, permease component AraH BUA36_RS29215
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 BUA36_RS02205 BUA36_RS22420
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) BUA36_RS11790 BUA36_RS13070
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) BUA36_RS29215
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) BUA36_RS29215
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 BUA36_RS11790 BUA36_RS13070
gguB L-arabinose ABC transporter, permease component GguB BUA36_RS11785
glcB malate synthase BUA36_RS28060
gyaR glyoxylate reductase BUA36_RS05860 BUA36_RS24285
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) BUA36_RS20895
xacI L-arabinose ABC transporter, permease component 2 (XacI) BUA36_RS21475
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) BUA36_RS20915 BUA36_RS01000
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BUA36_RS01000 BUA36_RS21470
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG BUA36_RS11790 BUA36_RS29220
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 24 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:

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