GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Escherichia coli BW25113

Best path

manX, manY, manZ, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manX glucosamine PTS system, EII-AB component ManX b1817
manY glucosamine PTS system, EII-C component ManY b1818
manZ glucosamine PTS system, EII-D component ManZ b1819 b3140
nagB glucosamine 6-phosphate deaminase (isomerizing) b0678 b3136
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 b0810 b1918
AO353_21720 glucosaminate ABC transporter, permease component 2 b0810 b1918
AO353_21725 glucosaminate ABC transporter, ATPase component b0809 b3271
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr b2417 b0679
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) b0679 b1101
gdh quinoprotein glucose dehydrogenase b0124 b0837
glc-kinase glucosamine kinase b2388
glucosaminate-lyase glucosaminate ammonia-lyase b0888 b0606
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 b1850 b4477
kdgK 2-keto-3-deoxygluconate kinase b3526
nag3 N-acetylglucosamine transporter nag3/nag4
nagA N-acetylglucosamine 6-phosphate deacetylase b0677
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components b0679 b1101
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components b0679 b1101
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) b0679 b1101
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) b2416 b3947
nagK N-acetylglucosamine kinase b1119 b0394
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP b0679 b1101
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) b1312
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB b1101 b1621
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC b0679 b1101
SLC2A2 glucosamine transporter SLC2A2 b2943
SM_b21216 ABC transporter for D-Glucosamine, ATPase component b3450 b4035
SM_b21219 ABC transporter for D-Glucosamine, permease component 1
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 b4033
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component b4035 b3450
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 b1312
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 b4033
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