GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Klebsiella michiganensis M5al

Best path

araF, araG, araH, araA, araB, araD

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF BWI76_RS18250
araG L-arabinose ABC transporter, ATPase component AraG BWI76_RS18245 BWI76_RS07240
araH L-arabinose ABC transporter, permease component AraH BWI76_RS18240 BWI76_RS14865
araA L-arabinose isomerase BWI76_RS04585
araB ribulokinase BWI76_RS04590
araD L-ribulose-5-phosphate epimerase BWI76_RS04580 BWI76_RS27115
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BWI76_RS13210 BWI76_RS05620
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit BWI76_RS17570
araE L-arabinose:H+ symporter BWI76_RS23425 BWI76_RS24055
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) BWI76_RS02795 BWI76_RS07235
araV L-arabinose ABC transporter, ATPase component AraV BWI76_RS06035 BWI76_RS03270
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) BWI76_RS02800 BWI76_RS07240
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) BWI76_RS02805 BWI76_RS14865
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) BWI76_RS02810 BWI76_RS00280
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE BWI76_RS27030
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA BWI76_RS27035 BWI76_RS07240
gguB L-arabinose ABC transporter, permease component GguB BWI76_RS27040 BWI76_RS14865
glcB malate synthase BWI76_RS01660
gyaR glyoxylate reductase BWI76_RS26960 BWI76_RS27925
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacB L-arabinose 1-dehydrogenase BWI76_RS07640 BWI76_RS13720
xacC L-arabinono-1,4-lactonase BWI76_RS21760 BWI76_RS23720
xacD L-arabinonate dehydratase BWI76_RS18100 BWI76_RS00975
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase
xacF alpha-ketoglutarate semialdehyde dehydrogenase BWI76_RS05620 BWI76_RS07615
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH) BWI76_RS23380
xacI L-arabinose ABC transporter, permease component 2 (XacI)
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) BWI76_RS01840 BWI76_RS17830
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) BWI76_RS26290 BWI76_RS23390
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG BWI76_RS14600 BWI76_RS00275
xylHsa L-arabinose ABC transporter, permease component XylH BWI76_RS00280 BWI76_RS00650

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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