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 (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