GapMind for catabolism of small carbon sources

 

D-lactate catabolism in Phaeobacter inhibens BS107

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 PGA1_c12640 PGA1_c16530
PGA1_c12650 D-lactate ABC transporter, permease component 1 PGA1_c12650
PGA1_c12660 D-lactate ABC transporter, permease component 2 PGA1_c12660
PGA1_c12670 D-lactate ABC transporter, substrate-binding component PGA1_c12670
glcD D-lactate dehydrogenase, FAD-linked subunit 1 (GlcD) PGA1_c29720 PGA1_c28240
glcE D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) PGA1_c29710
glcF D-lactate dehydrogenase, FeS subunit GlcF PGA1_c29700
Alternative steps:
D-LDH D-lactate dehydrogenase PGA1_c28240 PGA1_c06340
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 PGA1_c01240
lctD D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component PGA1_c28240 PGA1_c29720
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