GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

araF, araG, araH, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araF L-arabinose ABC transporter, substrate-binding component AraF H281DRAFT_06297 H281DRAFT_02332
araG L-arabinose ABC transporter, ATPase component AraG H281DRAFT_06298 H281DRAFT_02331
araH L-arabinose ABC transporter, permease component AraH H281DRAFT_06299 H281DRAFT_02330
xacB L-arabinose 1-dehydrogenase H281DRAFT_06300 H281DRAFT_06296
xacC L-arabinono-1,4-lactonase H281DRAFT_06301 H281DRAFT_01183
xacD L-arabinonate dehydratase H281DRAFT_02329 H281DRAFT_06137
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase H281DRAFT_03220
xacF alpha-ketoglutarate semialdehyde dehydrogenase H281DRAFT_01155 H281DRAFT_05316
Alternative steps:
aldA (glycol)aldehyde dehydrogenase H281DRAFT_00972 H281DRAFT_03540
aldox-large (glycol)aldehyde oxidoreductase, large subunit H281DRAFT_02182 H281DRAFT_02676
aldox-med (glycol)aldehyde oxidoreductase, medium subunit H281DRAFT_02674 H281DRAFT_01140
aldox-small (glycol)aldehyde oxidoreductase, small subunit H281DRAFT_02181 H281DRAFT_02675
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
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) H281DRAFT_05269 H281DRAFT_02173
araV L-arabinose ABC transporter, ATPase component AraV H281DRAFT_01260 H281DRAFT_02040
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) H281DRAFT_02174 H281DRAFT_05270
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) H281DRAFT_05271 H281DRAFT_02175
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) H281DRAFT_05272 H281DRAFT_02176
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE H281DRAFT_03877
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA H281DRAFT_03878 H281DRAFT_03380
gguB L-arabinose ABC transporter, permease component GguB H281DRAFT_03879 H281DRAFT_00427
glcB malate synthase H281DRAFT_00963 H281DRAFT_00576
gyaR glyoxylate reductase H281DRAFT_04333 H281DRAFT_06500
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) H281DRAFT_00167 H281DRAFT_02631
xacI L-arabinose ABC transporter, permease component 2 (XacI) H281DRAFT_00168
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) H281DRAFT_03749 H281DRAFT_04155
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) H281DRAFT_05701 H281DRAFT_03749
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG H281DRAFT_03224 H281DRAFT_04460
xylHsa L-arabinose ABC transporter, permease component XylH H281DRAFT_01120 H281DRAFT_02714

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, 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