GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Acidovorax sp. GW101-3H11

Best path

gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF

Also see fitness data for the top candidates

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA Ac3H11_609 Ac3H11_2881
gguB L-arabinose ABC transporter, permease component GguB Ac3H11_608
chvE L-arabinose ABC transporter, substrate-binding component ChvE Ac3H11_610
xacB L-arabinose 1-dehydrogenase Ac3H11_614 Ac3H11_2257
xacC L-arabinono-1,4-lactonase Ac3H11_615 Ac3H11_2081
xacD L-arabinonate dehydratase Ac3H11_604 Ac3H11_3523
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase Ac3H11_603
xacF alpha-ketoglutarate semialdehyde dehydrogenase Ac3H11_612 Ac3H11_255
Alternative steps:
aldA (glycol)aldehyde dehydrogenase Ac3H11_1480 Ac3H11_1496
aldox-large (glycol)aldehyde oxidoreductase, large subunit Ac3H11_3591
aldox-med (glycol)aldehyde oxidoreductase, medium subunit Ac3H11_3592
aldox-small (glycol)aldehyde oxidoreductase, small subunit Ac3H11_3590 Ac3H11_3428
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG Ac3H11_609 Ac3H11_607
araH L-arabinose ABC transporter, permease component AraH Ac3H11_1841 Ac3H11_2880
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) Ac3H11_2065
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) Ac3H11_611
araV L-arabinose ABC transporter, ATPase component AraV Ac3H11_4785 Ac3H11_2941
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) Ac3H11_607 Ac3H11_609
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) Ac3H11_606 Ac3H11_3036
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) Ac3H11_605 Ac3H11_2880
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase Ac3H11_4835
gyaR glyoxylate reductase Ac3H11_2599 Ac3H11_2341
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) Ac3H11_2064
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) Ac3H11_2066 Ac3H11_1610
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) Ac3H11_2066 Ac3H11_4785
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG Ac3H11_3037 Ac3H11_2881
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 17 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