GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Phaeobacter inhibens BS107

Best path

nagX, SMc02869, SMc02872, SMc02871, SMc02873, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagX transmembrane glucosamine N-acetyltransferase NagX
SMc02869 N-acetylglucosamine ABC transporter, ATPase component PGA1_c27970 PGA1_c13180
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 PGA1_c27940 PGA1_c07870
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 PGA1_c27950 PGA1_c16690
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component PGA1_c27930
nagK N-acetylglucosamine kinase PGA1_c27910
nagA N-acetylglucosamine 6-phosphate deacetylase PGA1_c27880
nagB glucosamine 6-phosphate deaminase (isomerizing) PGA1_c27890 PGA1_c10230
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 PGA1_c26600 PGA1_262p02370
AO353_21720 glucosaminate ABC transporter, permease component 2 PGA1_c02000 PGA1_262p02370
AO353_21725 glucosaminate ABC transporter, ATPase component PGA1_262p02350 PGA1_c11580
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase PGA1_c15880
glc-kinase glucosamine kinase
glucosaminate-lyase glucosaminate ammonia-lyase PGA1_c24780
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 PGA1_c28010 PGA1_c07350
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
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP)
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) PGA1_c23500
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) PGA1_c16700 PGA1_c07410
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) PGA1_c27950 PGA1_c07400
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 PGA1_c19470 PGA1_78p00190
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 PGA1_c16690 PGA1_c13190
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 PGA1_c16700 PGA1_c07870
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein

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, 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