GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Chryseobacterium arthrosphaerae CC-VM-7

Best path

Echvi_1880, araA, araB, araD

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Echvi_1880 L-arabinose:Na+ symporter BBI00_RS08940
araA L-arabinose isomerase BBI00_RS08950
araB ribulokinase BBI00_RS08960
araD L-ribulose-5-phosphate epimerase BBI00_RS08955
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BBI00_RS10955 BBI00_RS14510
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG
araH L-arabinose ABC transporter, permease component AraH
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 BBI00_RS09790 BBI00_RS03235
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh)
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh)
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE
gguA L-arabinose ABC transporter, ATPase component GguA
gguB L-arabinose ABC transporter, permease component GguB
glcB malate synthase BBI00_RS12690
gyaR glyoxylate reductase BBI00_RS08430 BBI00_RS02370
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase BBI00_RS16110 BBI00_RS19945
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase BBI00_RS01315
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase BBI00_RS10955 BBI00_RS04765
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) BBI00_RS20685 BBI00_RS20460
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BBI00_RS20685 BBI00_RS03235
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG BBI00_RS09790 BBI00_RS09085
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