GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Rhodobacter ovatus JA234

Best path

araE, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter
araA L-arabinose isomerase
araB ribulokinase CRO07_RS10595
araD L-ribulose-5-phosphate epimerase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase CRO07_RS00170 CRO07_RS10080
aldox-large (glycol)aldehyde oxidoreductase, large subunit CRO07_RS09145
aldox-med (glycol)aldehyde oxidoreductase, medium subunit CRO07_RS09150
aldox-small (glycol)aldehyde oxidoreductase, small subunit CRO07_RS09140 CRO07_RS16090
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG CRO07_RS00325 CRO07_RS12930
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 CRO07_RS11575 CRO07_RS12955
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) CRO07_RS00325 CRO07_RS12930
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
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA CRO07_RS00325 CRO07_RS16105
gguB L-arabinose ABC transporter, permease component GguB CRO07_RS10605
glcB malate synthase CRO07_RS05110 CRO07_RS06545
gyaR glyoxylate reductase CRO07_RS10960 CRO07_RS11825
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase CRO07_RS04670 CRO07_RS14205
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase CRO07_RS16225 CRO07_RS01200
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase CRO07_RS10080 CRO07_RS00170
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) CRO07_RS11575 CRO07_RS01810
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) CRO07_RS11575 CRO07_RS01810
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG CRO07_RS09955 CRO07_RS10610
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