GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Pseudomonas fluorescens FW300-N1B4

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gdh quinoprotein glucose dehydrogenase Pf1N1B4_821 Pf1N1B4_5582
AO353_21715 glucosaminate ABC transporter, permease component 1 Pf1N1B4_5644 Pf1N1B4_1713
AO353_21720 glucosaminate ABC transporter, permease component 2 Pf1N1B4_5643 Pf1N1B4_1712
AO353_21725 glucosaminate ABC transporter, ATPase component Pf1N1B4_5642 Pf1N1B4_1640
AO353_21710 glucosaminate ABC transporter, substrate-binding component Pf1N1B4_5645
glucosaminate-lyase glucosaminate ammonia-lyase Pf1N1B4_5639 Pf1N1B4_1046
kdgK 2-keto-3-deoxygluconate kinase Pf1N1B4_5638 Pf1N1B4_4765
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 Pf1N1B4_587 Pf1N1B4_399
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr Pf1N1B4_833
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
glc-kinase glucosamine kinase Pf1N1B4_600
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
nagB glucosamine 6-phosphate deaminase (isomerizing) Pf1N1B4_1947
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) Pf1N1B4_833
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) Pf1N1B4_833 Pf1N1B4_1146
nagK N-acetylglucosamine kinase Pf1N1B4_600
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP
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) Pf1N1B4_5114
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
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component Pf1N1B4_593 Pf1N1B4_4847
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 Pf1N1B4_5114 Pf1N1B4_4848
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 Pf1N1B4_5113
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component Pf1N1B4_5115 Pf1N1B4_4847
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 Pf1N1B4_5114 Pf1N1B4_594
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