GapMind for catabolism of small carbon sources


L-lactate catabolism in Azospirillum brasilense Sp245

Best path

lctP, lutA, lutB, lutC

Also see fitness data for the top candidates


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

19 steps (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lctP L-lactate:H+ symporter LctP or LidP AZOBR_RS25125
lutA L-lactate dehydrogenase, LutA subunit AZOBR_RS25115 AZOBR_RS01615
lutB L-lactate dehydrogenase, LutB subunit AZOBR_RS25110 AZOBR_RS01620
lutC L-lactate dehydrogenase, LutC subunit AZOBR_RS25105 AZOBR_RS01625
Alternative steps:
ackA acetate kinase AZOBR_RS12495 AZOBR_RS04605
acs acetyl-CoA synthetase, AMP-forming AZOBR_RS00270 AZOBR_RS06340
DVU3032 L-lactate dehydrogenase, LutC-like component AZOBR_RS01625 AZOBR_RS01620
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components AZOBR_RS25110 AZOBR_RS01620
L-LDH L-lactate dehydrogenase AZOBR_RS01310 AZOBR_RS14060
larD D,L-lactic acid transporter LarD
lctO L-lactate oxidase or 2-monooxygenase AZOBR_RS19085 AZOBR_RS27055
lldE L-lactate dehydrogenase, LldE subunit AZOBR_RS01615 AZOBR_RS25115
lldF L-lactate dehydrogenase, LldF subunit AZOBR_RS25110 AZOBR_RS01620
lldG L-lactate dehydrogenase, LldG subunit
mctP D,L-lactic acid transporter MctP
pta phosphate acetyltransferase AZOBR_RS04600 AZOBR_RS12500
SfMCT L-lactate transporter SfMCT AZOBR_RS07945 AZOBR_RS07885
Shew_2731 L-lactate:Na+ symporter, large component AZOBR_RS02940 AZOBR_RS19235
Shew_2732 L-lactate:Na+ symporter, small component

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.



Related tools

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