GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Chromobacterium vaccinii MWU205

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 (22 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 VL52_RS20940 VL52_RS07105
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit VL52_RS19360
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG VL52_RS18715
araH L-arabinose ABC transporter, permease component AraH VL52_RS18720
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) VL52_RS08415
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) VL52_RS18725
araV L-arabinose ABC transporter, ATPase component AraV VL52_RS13280 VL52_RS18065
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) VL52_RS18715 VL52_RS07675
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) VL52_RS18720
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) VL52_RS18720
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 VL52_RS18715 VL52_RS07675
gguB L-arabinose ABC transporter, permease component GguB VL52_RS18720
glcB malate synthase VL52_RS03490
gyaR glyoxylate reductase VL52_RS16495 VL52_RS02475
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase VL52_RS17095 VL52_RS01235
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase VL52_RS11430
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase VL52_RS09525 VL52_RS20020
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH) VL52_RS04905
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) VL52_RS12740 VL52_RS04920
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) VL52_RS12740 VL52_RS04920
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG VL52_RS18715 VL52_RS07675
xylHsa L-arabinose ABC transporter, permease component XylH VL52_RS18720

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