GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Dinoroseobacter shibae DFL-12

Best path

gamP, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
nagB glucosamine 6-phosphate deaminase (isomerizing) Dshi_1293
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 Dshi_0320
AO353_21725 glucosaminate ABC transporter, ATPase component Dshi_2221 Dshi_0321
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gdh quinoprotein glucose dehydrogenase Dshi_2294 Dshi_1523
glc-kinase glucosamine kinase Dshi_2001 Dshi_2797
glucosaminate-lyase glucosaminate ammonia-lyase Dshi_2654 Dshi_1935
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 Dshi_1768 Dshi_1241
kdgK 2-keto-3-deoxygluconate kinase Dshi_1268 Dshi_2797
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
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) Dshi_2062
nagK N-acetylglucosamine kinase Dshi_1655
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP
nagX transmembrane glucosamine N-acetyltransferase NagX
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) Dshi_1247
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) Dshi_1246 Dshi_2016
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 Dshi_1250 Dshi_0546
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 Dshi_3142 Dshi_0972
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 Dshi_3143 Dshi_1354
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component Dshi_0971 Dshi_1357
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 Dshi_0549 Dshi_1246
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