N-acetyl-D-glucosamine catabolism in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

N-acetyl-D-glucosamine catabolism in Klebsiella michiganensis M5al

Best path

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.

all: NAG-utilization
NAG-utilization:

NAG-PTS, nagA and nagB
or NAG-transport, nagK, nagA and nagB
Comment: Both pathways involve N-acetylglucosamine 6-phosphate, followed by deacetylase nagA and the isomerizing deaminase nagB, which produces fructose 6-phosphate, a central metabolic intermediate.

NAG-transport:

SMc02869, SMc02872, SMc02871 and SMc02873
or ngcE, ngcF and ngcG
or nagP
or nag3
or ngt1
Comment: Transporters were identified using: query: transporter:N-acetylglucosamine:N-ACETYL-D-GLUCOSAMINE:CPD-12541

NAG-PTS:

nagEcba
or nagF and nagEcb
or crr, ptsB and ptsC
or nagEIIA and nagPcb
Comment: PTS systems form N-acetylglucosamine 6-phosphate

21 steps (16 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
nagEcba	N-acetylglucosamine phosphotransferase system, EII-CBA components	BWI76_RS08220	BWI76_RS11130
nagA	N-acetylglucosamine 6-phosphate deacetylase	BWI76_RS08210
nagB	glucosamine 6-phosphate deaminase (isomerizing)	BWI76_RS08215	BWI76_RS00120
Alternative steps:
crr	N-acetylglucosamine phosphotransferase system, EII-A component Crr	BWI76_RS07290	BWI76_RS20655
nag3	N-acetylglucosamine transporter nag3/nag4
nagEcb	N-acetylglucosamine phosphotransferase system, EII-CB components	BWI76_RS08220	BWI76_RS11130
nagEIIA	N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP)	BWI76_RS08220	BWI76_RS11130
nagF	N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF)	BWI76_RS20650	BWI76_RS10675
nagK	N-acetylglucosamine kinase	BWI76_RS11225	BWI76_RS20510
nagP	N-acetylglucosamine transporter NagP
nagPcb	N-acetylglucosamine phosphotransferase system, EII-CB component NagP	BWI76_RS08220	BWI76_RS11130
ngcE	N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF	N-acetylglucosamine ABC transporter, permease component 1 (NgcF)	BWI76_RS23380	BWI76_RS03135
ngcG	N-acetylglucosamine ABC transporter, permease component 2 (NgcG)	BWI76_RS03130
ngt1	N-acetylglucosamine:H+ symporter Ngt1
ptsB	N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB	BWI76_RS11130	BWI76_RS08220
ptsC	N-acetylglucosamine phosphotransferase system, EII-C component PtsC	BWI76_RS08220	BWI76_RS11130
SMc02869	N-acetylglucosamine ABC transporter, ATPase component	BWI76_RS06690	BWI76_RS01840
SMc02871	N-acetylglucosamine ABC transporter, permease component 2	BWI76_RS17835
SMc02872	N-acetylglucosamine ABC transporter, permease component 1	BWI76_RS03135
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources