GapMind for catabolism of small carbon sources

 

D-lactate catabolism in Dinoroseobacter shibae DFL-12

Best path

PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF

Also see fitness data for the top candidates

Rules

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

14 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PGA1_c12640 D-lactate ABC transporter, ATP-binding component Dshi_1401 Dshi_3727
PGA1_c12650 D-lactate ABC transporter, permease component 1 Dshi_1402 Dshi_0860
PGA1_c12660 D-lactate ABC transporter, permease component 2 Dshi_1403 Dshi_3725
PGA1_c12670 D-lactate ABC transporter, substrate-binding component Dshi_1404
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) Dshi_2896 Dshi_1361
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) Dshi_2895 Dshi_2076
glcF D-lactate dehydrogenase, FeS subunit GlcF Dshi_2894
Alternative steps:
D-LDH D-lactate dehydrogenase Dshi_1361 Dshi_2076
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 Dshi_0216
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component Dshi_2896 Dshi_2076
lctP D-lactate:H+ symporter LctP or LidP
mctP D,L-lactic acid transporter

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 Aug 02 2021. The underlying query database was built on Aug 02 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