GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Desulfotomaculum ruminis DSM 2154

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 (19 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 DESRU_RS09115
Alternative steps:
aldA (glycol)aldehyde dehydrogenase DESRU_RS17700 DESRU_RS00445
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit DESRU_RS02650
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG DESRU_RS19235 DESRU_RS07445
araH L-arabinose ABC transporter, permease component AraH DESRU_RS19230 DESRU_RS07450
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 DESRU_RS00220 DESRU_RS19415
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) DESRU_RS19235 DESRU_RS07445
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) DESRU_RS07450
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) DESRU_RS19230 DESRU_RS07450
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 DESRU_RS07445 DESRU_RS19235
gguB L-arabinose ABC transporter, permease component GguB DESRU_RS19230 DESRU_RS07450
glcB malate synthase
gyaR glyoxylate reductase DESRU_RS12195 DESRU_RS02775
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase DESRU_RS08830 DESRU_RS12245
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase DESRU_RS12190 DESRU_RS01855
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase DESRU_RS02740 DESRU_RS17700
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) DESRU_RS15860 DESRU_RS19415
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) DESRU_RS19415 DESRU_RS15860
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG DESRU_RS19235 DESRU_RS07445
xylHsa L-arabinose ABC transporter, permease component XylH DESRU_RS19230

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