GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Phaeobacter inhibens BS107

Best path

araE, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter
xacB L-arabinose 1-dehydrogenase PGA1_c07370 PGA1_c13170
xacC L-arabinono-1,4-lactonase PGA1_c07340
xacD L-arabinonate dehydratase PGA1_c07380 PGA1_c04540
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase PGA1_c05130 PGA1_262p01460
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PGA1_c29650 PGA1_c23170
aldox-large (glycol)aldehyde oxidoreductase, large subunit PGA1_c20870 PGA1_c11660
aldox-med (glycol)aldehyde oxidoreductase, medium subunit PGA1_c20860
aldox-small (glycol)aldehyde oxidoreductase, small subunit PGA1_c20880 PGA1_c16210
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG PGA1_c23060 PGA1_c03960
araH L-arabinose ABC transporter, permease component AraH
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 PGA1_c02740 PGA1_c07900
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) PGA1_c23060 PGA1_c26910
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh)
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) PGA1_c28050 PGA1_c23080
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 PGA1_c23060 PGA1_c03960
gguB L-arabinose ABC transporter, permease component GguB PGA1_262p00440
glcB malate synthase PGA1_c09900 PGA1_c03680
gyaR glyoxylate reductase PGA1_c28260 PGA1_c24680
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) PGA1_78p00170 PGA1_c19490
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) PGA1_c27320 PGA1_c02740
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) PGA1_c02740 PGA1_c16680
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG PGA1_262p00450 PGA1_c28040
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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