GapMind for catabolism of small carbon sources


D-glucosamine (chitosamine) catabolism in Pseudomonas fluorescens GW456-L13

Best path

gamP, nagB

Also see fitness data for the top candidates


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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) PfGW456L13_4833
nagB glucosamine 6-phosphate deaminase (isomerizing) PfGW456L13_4831 PfGW456L13_686
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 PfGW456L13_445 PfGW456L13_3607
AO353_21720 glucosaminate ABC transporter, permease component 2 PfGW456L13_445 PfGW456L13_4636
AO353_21725 glucosaminate ABC transporter, ATPase component PfGW456L13_376 PfGW456L13_876
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr PfGW456L13_4832
gdh quinoprotein glucose dehydrogenase PfGW456L13_4805 PfGW456L13_1173
glc-kinase glucosamine kinase PfGW456L13_1890
glucosaminate-lyase glucosaminate ammonia-lyase PfGW456L13_2867 PfGW456L13_4983
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC: PfGW456L13_1903 PfGW456L13_2127
kdgK 2-keto-3-deoxygluconate kinase PfGW456L13_2869 PfGW456L13_2950
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
nagA N-acetylglucosamine 6-phosphate deacetylase PfGW456L13_4830
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components PfGW456L13_4833
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components PfGW456L13_4833
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) PfGW456L13_4833 PfGW456L13_4832
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) PfGW456L13_4832 PfGW456L13_5075
nagK N-acetylglucosamine kinase PfGW456L13_1890
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP PfGW456L13_4833
nagX transmembrane glucosamine N-acetyltransferase NagX
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
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC PfGW456L13_4833
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component PfGW456L13_1897 PfGW456L13_3039
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 PfGW456L13_3040
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 PfGW456L13_3039 PfGW456L13_1897
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 PfGW456L13_1896
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.



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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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