GapMind for catabolism of small carbon sources


D-glucosamine (chitosamine) catabolism in Ruegeria conchae TW15

Best path

nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB


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
nagX transmembrane glucosamine N-acetyltransferase NagX
SMc02869 N-acetylglucosamine ABC transporter, ATPase component G7G_RS0105580 G7G_RS0120425
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 G7G_RS0105595
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 G7G_RS0105590 G7G_RS0115540
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component G7G_RS0105600
nagK N-acetylglucosamine kinase G7G_RS0105610
nagA N-acetylglucosamine 6-phosphate deacetylase G7G_RS0105625
nagB glucosamine 6-phosphate deaminase (isomerizing) G7G_RS0105620 G7G_RS0117720
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 G7G_RS0111055 G7G_RS0111530
AO353_21720 glucosaminate ABC transporter, permease component 2 G7G_RS0111530 G7G_RS0111055
AO353_21725 glucosaminate ABC transporter, ATPase component G7G_RS0105150 G7G_RS0101315
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase G7G_RS0107420
glc-kinase glucosamine kinase G7G_RS0111340
glucosaminate-lyase glucosaminate ammonia-lyase G7G_RS0112640
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC: G7G_RS0112140 G7G_RS0100605
kdgK 2-keto-3-deoxygluconate kinase G7G_RS0119975 G7G_RS0117160
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)
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) G7G_RS0111290
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) G7G_RS0105590 G7G_RS0120420
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 G7G_RS0103685 G7G_RS0121175
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 G7G_RS0110560 G7G_RS0120420
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 G7G_RS0115545
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 24 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 (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