GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Rhodobacter viridis JA737

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase C8J30_RS08590 C8J30_RS06315
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit C8J30_RS07995
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG C8J30_RS10885 C8J30_RS14105
araH L-arabinose ABC transporter, permease component AraH C8J30_RS10880 C8J30_RS14100
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) C8J30_RS14095
araV L-arabinose ABC transporter, ATPase component AraV C8J30_RS08100 C8J30_RS01990
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) C8J30_RS14105 C8J30_RS10885
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) C8J30_RS10880 C8J30_RS14100
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) C8J30_RS14100 C8J30_RS10880
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE C8J30_RS13470
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA C8J30_RS14105 C8J30_RS10885
gguB L-arabinose ABC transporter, permease component GguB C8J30_RS04455
glcB malate synthase C8J30_RS16380 C8J30_RS07675
gyaR glyoxylate reductase C8J30_RS06910 C8J30_RS11315
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase C8J30_RS14495 C8J30_RS03120
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase C8J30_RS14975 C8J30_RS09805
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase C8J30_RS06315 C8J30_RS08590
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) C8J30_RS03245 C8J30_RS01990
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) C8J30_RS01990 C8J30_RS08100
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG C8J30_RS03205 C8J30_RS04460
xylHsa L-arabinose ABC transporter, permease component XylH C8J30_RS14100

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