GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Azospirillum brasilense Sp245

Best path

gguA, gguB, chvE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB

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 AZOBR_RS31245 AZOBR_RS31210
gguB L-arabinose ABC transporter, permease component GguB AZOBR_RS31250
chvE L-arabinose ABC transporter, substrate-binding component ChvE AZOBR_RS31240
xacB L-arabinose 1-dehydrogenase AZOBR_RS31255 AZOBR_RS29790
xacC L-arabinono-1,4-lactonase AZOBR_RS31230 AZOBR_RS22710
xacD L-arabinonate dehydratase AZOBR_RS31260 AZOBR_RS25270
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
aldA (glycol)aldehyde dehydrogenase AZOBR_RS19635 AZOBR_RS09720
gyaR glyoxylate reductase AZOBR_RS01325 AZOBR_RS15695
glcB malate synthase AZOBR_RS03245 AZOBR_RS25430
Alternative steps:
aldox-large (glycol)aldehyde oxidoreductase, large subunit AZOBR_RS08560 AZOBR_RS06730
aldox-med (glycol)aldehyde oxidoreductase, medium subunit AZOBR_RS08555 AZOBR_RS29695
aldox-small (glycol)aldehyde oxidoreductase, small subunit AZOBR_RS08565 AZOBR_RS27485
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase AZOBR_RS05280
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG AZOBR_RS31210 AZOBR_RS31245
araH L-arabinose ABC transporter, permease component AraH AZOBR_RS27940
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) AZOBR_RS31215
araV L-arabinose ABC transporter, ATPase component AraV AZOBR_RS24710 AZOBR_RS08840
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) AZOBR_RS31210 AZOBR_RS31245
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) AZOBR_RS31205
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) AZOBR_RS31200 AZOBR_RS27940
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase AZOBR_RS18165 AZOBR_RS29750
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH) AZOBR_RS27990 AZOBR_RS00070
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) AZOBR_RS00060 AZOBR_RS27980
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) AZOBR_RS00060 AZOBR_RS27980
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG AZOBR_RS31210 AZOBR_RS31880
xylHsa L-arabinose ABC transporter, permease component XylH AZOBR_RS27940

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.

Links

Downloads

Related tools

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