GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Halomonas desiderata SP1

Best path

araF, araG, araH, xacB, xacC, xacD, xacE, xacF

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF BZY95_RS16550
araG L-arabinose ABC transporter, ATPase component AraG BZY95_RS16555 BZY95_RS00745
araH L-arabinose ABC transporter, permease component AraH BZY95_RS16560
xacB L-arabinose 1-dehydrogenase BZY95_RS16540 BZY95_RS16600
xacC L-arabinono-1,4-lactonase BZY95_RS16655 BZY95_RS16570
xacD L-arabinonate dehydratase BZY95_RS16565 BZY95_RS16650
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase BZY95_RS16535
xacF alpha-ketoglutarate semialdehyde dehydrogenase BZY95_RS06200 BZY95_RS14765
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BZY95_RS15485 BZY95_RS20815
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit BZY95_RS20185
aldox-small (glycol)aldehyde oxidoreductase, small subunit BZY95_RS17660 BZY95_RS15850
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter BZY95_RS16640
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 BZY95_RS11680 BZY95_RS15925
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) BZY95_RS16555
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh)
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
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 BZY95_RS16555
gguB L-arabinose ABC transporter, permease component GguB BZY95_RS16560
glcB malate synthase BZY95_RS06550
gyaR glyoxylate reductase BZY95_RS06210 BZY95_RS01720
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) BZY95_RS15415
xacI L-arabinose ABC transporter, permease component 2 (XacI) BZY95_RS15420
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) BZY95_RS15425 BZY95_RS17245
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BZY95_RS17245 BZY95_RS11680
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG BZY95_RS16555 BZY95_RS12910
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 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