GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Shewanella loihica PV-4

Best path

nagX, nagP, nagK, nagA, nagB

Also see fitness data for the top candidates

Rules

Overview: The canonical pathway for glucosamine utilization involves glucosamine 6-phosphate as an intermediate, as in N-acetylglucosamine utilization (link). GapMind also includes two other pathways: an oxidative pathway via glucosaminate ammonia-lyase, and a transmembrane transacetylase (NagX) pathway.

40 steps (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagX transmembrane glucosamine N-acetyltransferase NagX Shew_1118
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:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 Shew_3165
AO353_21720 glucosaminate ABC transporter, permease component 2
AO353_21725 glucosaminate ABC transporter, ATPase component Shew_3164 Shew_0974
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) Shew_2641
gdh quinoprotein glucose dehydrogenase
glc-kinase glucosamine kinase Shew_1116 Shew_1428
glucosaminate-lyase glucosaminate ammonia-lyase Shew_2028 Shew_0793
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 Shew_2045
kdgK 2-keto-3-deoxygluconate kinase
manX glucosamine PTS system, EII-AB component ManX
manY glucosamine PTS system, EII-C component ManY
manZ glucosamine PTS system, EII-D component ManZ
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
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component Shew_0974 Shew_0863
SM_b21219 ABC transporter for D-Glucosamine, permease component 1
SM_b21220 ABC transporter for D-Glucosamine, permease component 2
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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 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, the preprint on GapMind for carbon sources, 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