GapMind for catabolism of small carbon sources

 

D-lactate catabolism in Knoellia flava TL1

Best path

mctP, D-LDH

Rules

Overview: D-lactate catabolism in GapMind is based on D-lactate dehydrogenases, which form pyruvate.

14 steps (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctP D,L-lactic acid transporter N798_RS06185
D-LDH D-lactate dehydrogenase N798_RS10165 N798_RS16845
Alternative steps:
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) N798_RS10165
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) N798_RS10165
glcF D-lactate dehydrogenase, FeS subunit GlcF
larD D,L-lactic acid transporter
lctB electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit
lctC electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit N798_RS16595
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component N798_RS10165
lctP D-lactate:H+ symporter LctP or LidP N798_RS07055
PGA1_c12640 D-lactate ABC transporter, ATP-binding component N798_RS04780 N798_RS14375
PGA1_c12650 D-lactate ABC transporter, permease component 1 N798_RS04800
PGA1_c12660 D-lactate ABC transporter, permease component 2
PGA1_c12670 D-lactate ABC transporter, substrate-binding 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