GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Gallaecimonas xiamenensis 3-C-1

Best path

nagX, nagP, nagK, nagA, nagB

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagX transmembrane glucosamine N-acetyltransferase NagX B3C1_RS03130
nagP N-acetylglucosamine transporter NagP B3C1_RS06620 B3C1_RS01975
nagK N-acetylglucosamine kinase B3C1_RS06605 B3C1_RS01960
nagA N-acetylglucosamine 6-phosphate deacetylase B3C1_RS06615 B3C1_RS01965
nagB glucosamine 6-phosphate deaminase (isomerizing) B3C1_RS06610 B3C1_RS01955
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1
AO353_21720 glucosaminate ABC transporter, permease component 2
AO353_21725 glucosaminate ABC transporter, ATPase component B3C1_RS03280 B3C1_RS04305
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr B3C1_RS04845
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) B3C1_RS15380
gdh quinoprotein glucose dehydrogenase B3C1_RS03040
glc-kinase glucosamine kinase B3C1_RS03115 B3C1_RS06605
glucosaminate-lyase glucosaminate ammonia-lyase B3C1_RS00985 B3C1_RS14505
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 B3C1_RS03510 B3C1_RS16160
kdgK 2-keto-3-deoxygluconate kinase B3C1_RS16155
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 B3C1_RS15380
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components B3C1_RS15380
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) B3C1_RS15380 B3C1_RS04845
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) B3C1_RS04850 B3C1_RS17340
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP B3C1_RS15380
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 B3C1_RS15380
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC B3C1_RS15380
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component B3C1_RS04305 B3C1_RS03280
SM_b21219 ABC transporter for D-Glucosamine, permease component 1
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 B3C1_RS04305 B3C1_RS03280
SMc02871 N-acetylglucosamine ABC transporter, permease component 2
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 24 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 (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:

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