GapMind for catabolism of small carbon sources

 

Definition of N-acetyl-D-glucosamine catabolism

As rules and steps, or see full text

Rules

Overview: N-acetylglucosamine utilization in GapMind is based on MetaCyc pathways N-acetylglucosamine degradation I (link) and pathway II (link). These pathways differ in whether uptake and phosphorylation are performed by a PTS system or performed separately by a transporter and a kinase.

Steps

nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components

nagF: N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF)

nagEcb: N-acetylglucosamine phosphotransferase system, EII-CB components

crr: N-acetylglucosamine phosphotransferase system, EII-A component Crr

ptsB: N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB

ptsC: N-acetylglucosamine phosphotransferase system, EII-C component PtsC

nagEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP)

nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP

SMc02869: N-acetylglucosamine ABC transporter, ATPase component

SMc02872: N-acetylglucosamine ABC transporter, permease component 1

SMc02871: N-acetylglucosamine ABC transporter, permease component 2

SMc02873: N-acetylglucosamine ABC transporter, substrate-binding component

ngcE: N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)

ngcF: N-acetylglucosamine ABC transporter, permease component 1 (NgcF)

ngcG: N-acetylglucosamine ABC transporter, permease component 2 (NgcG)

nagP: N-acetylglucosamine transporter NagP

nag3: N-acetylglucosamine transporter nag3/nag4

ngt1: N-acetylglucosamine:H+ symporter Ngt1

nagA: N-acetylglucosamine 6-phosphate deacetylase

nagB: glucosamine 6-phosphate deaminase (isomerizing)

nagK: N-acetylglucosamine kinase

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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