GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

gguA, gguB, chvE, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA AU252_RS04575 AU252_RS09320
gguB L-arabinose ABC transporter, permease component GguB AU252_RS09325 AU252_RS04580
chvE L-arabinose ABC transporter, substrate-binding component ChvE AU252_RS09315 AU252_RS04585
araA L-arabinose isomerase AU252_RS22360
araB ribulokinase AU252_RS22370
araD L-ribulose-5-phosphate epimerase AU252_RS22365
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AU252_RS01005 AU252_RS01045
aldox-large (glycol)aldehyde oxidoreductase, large subunit AU252_RS20570
aldox-med (glycol)aldehyde oxidoreductase, medium subunit AU252_RS20560
aldox-small (glycol)aldehyde oxidoreductase, small subunit AU252_RS20565 AU252_RS13745
araE L-arabinose:H+ symporter AU252_RS05985 AU252_RS11015
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG AU252_RS09320 AU252_RS01705
araH L-arabinose ABC transporter, permease component AraH AU252_RS07275 AU252_RS01710
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) AU252_RS14695
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh)
araV L-arabinose ABC transporter, ATPase component AraV AU252_RS06475 AU252_RS13340
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) AU252_RS07280 AU252_RS09320
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) AU252_RS01710 AU252_RS07275
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) AU252_RS01710 AU252_RS07275
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase AU252_RS07205 AU252_RS00965
gyaR glyoxylate reductase AU252_RS16225 AU252_RS07215
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase AU252_RS01735 AU252_RS01630
xacC L-arabinono-1,4-lactonase
xacD L-arabinonate dehydratase AU252_RS19105 AU252_RS14175
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase AU252_RS14625 AU252_RS13420
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH) AU252_RS14430 AU252_RS14405
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) AU252_RS06475 AU252_RS11300
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) AU252_RS06475 AU252_RS13340
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG AU252_RS13295 AU252_RS08570
xylHsa L-arabinose ABC transporter, permease component XylH AU252_RS10085

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