GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Pseudomonas fluorescens FW300-N2C3

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gdh quinoprotein glucose dehydrogenase AO356_17600 AO356_30385
AO353_21715 glucosaminate ABC transporter, permease component 1 AO356_00475 AO356_12035
AO353_21720 glucosaminate ABC transporter, permease component 2 AO356_00470 AO356_10415
AO353_21725 glucosaminate ABC transporter, ATPase component AO356_00465 AO356_28625
AO353_21710 glucosaminate ABC transporter, substrate-binding component AO356_00480
glucosaminate-lyase glucosaminate ammonia-lyase AO356_00450 AO356_16715
kdgK 2-keto-3-deoxygluconate kinase AO356_28555 AO356_00445
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 AO356_05150 AO356_20285
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr AO356_17540
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) AO356_17535
glc-kinase glucosamine kinase AO356_05215
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 AO356_17550
nagB glucosamine 6-phosphate deaminase (isomerizing) AO356_17545 AO356_11740
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components AO356_17535
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components AO356_17535
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) AO356_17535 AO356_17540
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) AO356_17540 AO356_07335
nagK N-acetylglucosamine kinase AO356_05215
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP AO356_17535
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) AO356_28580
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB AO356_17535
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC AO356_17535
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component AO356_05180 AO356_27685
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 AO356_28580 AO356_27680
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 AO356_28575
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component AO356_00010 AO356_27685
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 AO356_28580
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, 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