GapMind for catabolism of small carbon sources

 

L-lactate catabolism in Streptacidiphilus oryzae TH49

Best path

mctP, lctO, acs

Rules

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

19 steps (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctP D,L-lactic acid transporter MctP BS73_RS15850
lctO L-lactate oxidase or 2-monooxygenase BS73_RS10185 BS73_RS07640
acs acetyl-CoA synthetase, AMP-forming BS73_RS20690 BS73_RS01530
Alternative steps:
ackA acetate kinase BS73_RS15005
DVU3032 L-lactate dehydrogenase, LutC-like component
DVU3033 L-lactate dehydrogenase, fused LutA/LutB components BS73_RS03925 BS73_RS10140
L-LDH L-lactate dehydrogenase BS73_RS07640 BS73_RS01430
larD D,L-lactic acid transporter LarD BS73_RS34080 BS73_RS10550
lctP L-lactate:H+ symporter LctP or LidP BS73_RS26640
lldE L-lactate dehydrogenase, LldE subunit BS73_RS10145 BS73_RS03920
lldF L-lactate dehydrogenase, LldF subunit BS73_RS10140 BS73_RS03925
lldG L-lactate dehydrogenase, LldG subunit
lutA L-lactate dehydrogenase, LutA subunit BS73_RS10145 BS73_RS03920
lutB L-lactate dehydrogenase, LutB subunit BS73_RS10140 BS73_RS03925
lutC L-lactate dehydrogenase, LutC subunit
pta phosphate acetyltransferase
SfMCT L-lactate transporter SfMCT
Shew_2731 L-lactate:Na+ symporter, large component BS73_RS06885
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 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