GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Marinobacter adhaerens HP15

Best path

Shew_2731, Shew_2732, lutA, lutB, lutC

Also see fitness data for the top candidates

Rules

Overview: L-lactate degradation in GapMind is based on L-lactate dehydrogenases or oxidases.

19 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Shew_2731 L-lactate:Na+ symporter, large component HP15_1251
Shew_2732 L-lactate:Na+ symporter, small component HP15_1252
lutA L-lactate dehydrogenase, LutA subunit HP15_4088 HP15_2886
lutB L-lactate dehydrogenase, LutB subunit HP15_4089 HP15_2887
lutC L-lactate dehydrogenase, LutC subunit HP15_4090 HP15_2888
Alternative steps:
ackA acetate kinase HP15_1245 HP15_1499
acs acetyl-CoA synthetase, AMP-forming HP15_811 HP15_2053
DVU3032 L-lactate dehydrogenase, LutC-like component HP15_2888 HP15_4090
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components HP15_4089 HP15_2887
L-LDH L-lactate dehydrogenase HP15_2710
larD D,L-lactic acid transporter LarD
lctO L-lactate oxidase or 2-monooxygenase
lctP L-lactate:H+ symporter LctP or LidP
lldE L-lactate dehydrogenase, LldE subunit HP15_2886 HP15_4088
lldF L-lactate dehydrogenase, LldF subunit HP15_2887 HP15_4089
lldG L-lactate dehydrogenase, LldG subunit HP15_2888
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase HP15_1498
SfMCT L-lactate transporter SfMCT

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