GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Halococcus hamelinensis 100A6

Best path

xacG, xacH, xacI, xacJ, xacK, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xacG L-arabinose ABC transporter, substrate-binding component XacG C447_RS16055
xacH L-arabinose ABC transporter, permease component 1 (XacH) C447_RS16060 C447_RS07645
xacI L-arabinose ABC transporter, permease component 2 (XacI) C447_RS16065
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) C447_RS16070 C447_RS16760
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) C447_RS16070 C447_RS16760
xacB L-arabinose 1-dehydrogenase C447_RS06330 C447_RS00650
xacC L-arabinono-1,4-lactonase C447_RS09600
xacD L-arabinonate dehydratase C447_RS02110 C447_RS13870
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase C447_RS01765 C447_RS14150
Alternative steps:
aldA (glycol)aldehyde dehydrogenase C447_RS14150 C447_RS12725
aldox-large (glycol)aldehyde oxidoreductase, large subunit C447_RS10570
aldox-med (glycol)aldehyde oxidoreductase, medium subunit C447_RS10565
aldox-small (glycol)aldehyde oxidoreductase, small subunit C447_RS10575
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter C447_RS08630
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG
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 C447_RS07635 C447_RS16070
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh)
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
gguB L-arabinose ABC transporter, permease component GguB
glcB malate synthase C447_RS01715 C447_RS06725
gyaR glyoxylate reductase C447_RS09330 C447_RS11630
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG C447_RS10700
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