GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) H281DRAFT_01976 H281DRAFT_01853
nagB glucosamine 6-phosphate deaminase (isomerizing) H281DRAFT_01978 H281DRAFT_05935
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component H281DRAFT_05870
AO353_21715 glucosaminate ABC transporter, permease component 1 H281DRAFT_00741 H281DRAFT_02614
AO353_21720 glucosaminate ABC transporter, permease component 2 H281DRAFT_05872 H281DRAFT_00741
AO353_21725 glucosaminate ABC transporter, ATPase component H281DRAFT_05297 H281DRAFT_00221
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr H281DRAFT_01852 H281DRAFT_01977
gdh quinoprotein glucose dehydrogenase H281DRAFT_03298 H281DRAFT_00328
glc-kinase glucosamine kinase H281DRAFT_00163 H281DRAFT_05731
glucosaminate-lyase glucosaminate ammonia-lyase H281DRAFT_01893 H281DRAFT_00173
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 H281DRAFT_06295 H281DRAFT_04277
kdgK 2-keto-3-deoxygluconate kinase H281DRAFT_00856 H281DRAFT_05211
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 H281DRAFT_01979 H281DRAFT_05506
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components H281DRAFT_01976 H281DRAFT_01853
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components H281DRAFT_01976 H281DRAFT_01853
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) H281DRAFT_01853 H281DRAFT_01976
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) H281DRAFT_01977 H281DRAFT_01852
nagK N-acetylglucosamine kinase H281DRAFT_05731 H281DRAFT_00163
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP H281DRAFT_01976 H281DRAFT_01853
nagX transmembrane glucosamine N-acetyltransferase NagX
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) H281DRAFT_02632 H281DRAFT_03232
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB H281DRAFT_01853
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC H281DRAFT_01976 H281DRAFT_01853
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component H281DRAFT_00169 H281DRAFT_03749
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 H281DRAFT_03745 H281DRAFT_04157
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 H281DRAFT_03746 H281DRAFT_05891
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component H281DRAFT_04155 H281DRAFT_02629
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 H281DRAFT_02632 H281DRAFT_03232
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, 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