GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Thioclava dalianensis DLFJ1-1

Best path

gguA, gguB, chvE, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gguA L-arabinose ABC transporter, ATPase component GguA DL1_RS09090 DL1_RS19810
gguB L-arabinose ABC transporter, permease component GguB DL1_RS09095 DL1_RS03530
chvE L-arabinose ABC transporter, substrate-binding component ChvE DL1_RS09085 DL1_RS17605
xacB L-arabinose 1-dehydrogenase DL1_RS09115 DL1_RS06015
xacC L-arabinono-1,4-lactonase DL1_RS05970 DL1_RS14505
xacD L-arabinonate dehydratase DL1_RS09105 DL1_RS12290
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase DL1_RS09100
xacF alpha-ketoglutarate semialdehyde dehydrogenase DL1_RS12240 DL1_RS09110
Alternative steps:
aldA (glycol)aldehyde dehydrogenase DL1_RS02130 DL1_RS11710
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit DL1_RS05775 DL1_RS04930
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araE L-arabinose:H+ symporter
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG DL1_RS17670 DL1_RS19810
araH L-arabinose ABC transporter, permease component AraH DL1_RS19800 DL1_RS17675
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) DL1_RS05835
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh) DL1_RS05955
araV L-arabinose ABC transporter, ATPase component AraV DL1_RS14470 DL1_RS14510
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) DL1_RS05950 DL1_RS17670
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh) DL1_RS05945 DL1_RS20305
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh) DL1_RS05940 DL1_RS17675
BT0355 L-arabinose:Na+ symporter
Echvi_1880 L-arabinose:Na+ symporter
glcB malate synthase DL1_RS01175
gyaR glyoxylate reductase DL1_RS07735 DL1_RS07935
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) DL1_RS05840 DL1_RS04145
xacI L-arabinose ABC transporter, permease component 2 (XacI) DL1_RS05835
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) DL1_RS04020 DL1_RS06010
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) DL1_RS14385 DL1_RS04020
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG DL1_RS03535 DL1_RS21830
xylHsa L-arabinose ABC transporter, permease component XylH DL1_RS15040 DL1_RS17680

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