GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gdh quinoprotein glucose dehydrogenase AO353_16045
AO353_21715 glucosaminate ABC transporter, permease component 1 AO353_21715 AO353_11600
AO353_21720 glucosaminate ABC transporter, permease component 2 AO353_21720 AO353_11605
AO353_21725 glucosaminate ABC transporter, ATPase component AO353_21725 AO353_28150
AO353_21710 glucosaminate ABC transporter, substrate-binding component AO353_21710 AO353_12320
glucosaminate-lyase glucosaminate ammonia-lyase AO353_21740 AO353_05015
kdgK 2-keto-3-deoxygluconate kinase AO353_21745 AO353_26875
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 AO353_03350 AO353_01265
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr AO353_04460 AO353_15995
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) AO353_04465
glc-kinase glucosamine kinase AO353_03415
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 AO353_04450
nagB glucosamine 6-phosphate deaminase (isomerizing) AO353_04455 AO353_10370
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components AO353_04465
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components AO353_04465
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) AO353_04465 AO353_15995
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) AO353_04460 AO353_15995
nagK N-acetylglucosamine kinase AO353_03415
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP AO353_04465
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) AO353_25125
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 AO353_04465
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component AO353_03380 AO353_25895
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 AO353_25125 AO353_25890
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 AO353_25120
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component AO353_25130 AO353_25895
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 AO353_25125 AO353_03385
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.

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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, 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