GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism in Shewanella loihica PV-4

Best path

nagP, nagK, nagA, nagB

Also see fitness data for the top candidates

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.

21 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagP N-acetylglucosamine transporter NagP Shew_1119
nagK N-acetylglucosamine kinase Shew_1116 Shew_1428
nagA N-acetylglucosamine 6-phosphate deacetylase Shew_1117
nagB glucosamine 6-phosphate deaminase (isomerizing) Shew_0815 Shew_3839
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
nag3 N-acetylglucosamine transporter nag3/nag4
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components Shew_2641
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components Shew_2641
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) Shew_2641 Shew_1864
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) Shew_1865 Shew_1039
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP Shew_2641
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)
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB Shew_2641
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC Shew_2641
SMc02869 N-acetylglucosamine ABC transporter, ATPase component Shew_0974 Shew_0863
SMc02871 N-acetylglucosamine ABC transporter, permease component 2
SMc02872 N-acetylglucosamine ABC transporter, permease component 1
SMc02873 N-acetylglucosamine 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 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