GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Dyella japonica UNC79MFTsu3.2

Best path

nagX, nagP, 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 N515DRAFT_0596 N515DRAFT_4388
nagP N-acetylglucosamine transporter NagP N515DRAFT_0592 N515DRAFT_1918
nagK N-acetylglucosamine kinase N515DRAFT_0593 N515DRAFT_0393
nagA N-acetylglucosamine 6-phosphate deacetylase N515DRAFT_0589
nagB glucosamine 6-phosphate deaminase (isomerizing) N515DRAFT_0590 N515DRAFT_4298
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 N515DRAFT_2043 N515DRAFT_1562
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase N515DRAFT_0461
glc-kinase glucosamine kinase N515DRAFT_4210 N515DRAFT_0393
glucosaminate-lyase glucosaminate ammonia-lyase N515DRAFT_2222 N515DRAFT_1348
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 N515DRAFT_3178 N515DRAFT_1232
kdgK 2-keto-3-deoxygluconate kinase N515DRAFT_2221
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) N515DRAFT_3957
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) N515DRAFT_3134
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) N515DRAFT_3133
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 N515DRAFT_4212 N515DRAFT_1562
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 N515DRAFT_3133
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 N515DRAFT_3134
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component N515DRAFT_4212 N515DRAFT_1562
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 N515DRAFT_3133
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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