GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Klebsiella michiganensis M5al

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manX glucosamine PTS system, EII-AB component ManX BWI76_RS17890
manY glucosamine PTS system, EII-C component ManY BWI76_RS17895 BWI76_RS01730
manZ glucosamine PTS system, EII-D component ManZ BWI76_RS17900 BWI76_RS01725
nagB glucosamine 6-phosphate deaminase (isomerizing) BWI76_RS08215 BWI76_RS00120
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 BWI76_RS08970 BWI76_RS14440
AO353_21720 glucosaminate ABC transporter, permease component 2 BWI76_RS08970 BWI76_RS16800
AO353_21725 glucosaminate ABC transporter, ATPase component BWI76_RS10370 BWI76_RS10585
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr BWI76_RS07290 BWI76_RS20655
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) BWI76_RS08220 BWI76_RS11130
gdh quinoprotein glucose dehydrogenase BWI76_RS04950 BWI76_RS13270
glc-kinase glucosamine kinase BWI76_RS20510 BWI76_RS11225
glucosaminate-lyase glucosaminate ammonia-lyase BWI76_RS03885 BWI76_RS09645
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 BWI76_RS18095 BWI76_RS27940
kdgK 2-keto-3-deoxygluconate kinase BWI76_RS26750 BWI76_RS26950
nag3 N-acetylglucosamine transporter nag3/nag4
nagA N-acetylglucosamine 6-phosphate deacetylase BWI76_RS08210
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components BWI76_RS08220 BWI76_RS11130
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components BWI76_RS08220 BWI76_RS11130
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) BWI76_RS08220 BWI76_RS11130
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) BWI76_RS20650 BWI76_RS10675
nagK N-acetylglucosamine kinase BWI76_RS11225 BWI76_RS20510
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP BWI76_RS08220 BWI76_RS11130
nagX transmembrane glucosamine N-acetyltransferase NagX
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) BWI76_RS23380 BWI76_RS03135
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) BWI76_RS03130
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB BWI76_RS11130 BWI76_RS08220
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC BWI76_RS08220 BWI76_RS11130
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component BWI76_RS17830 BWI76_RS26290
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 BWI76_RS01820
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 BWI76_RS03135 BWI76_RS23380
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component BWI76_RS06690 BWI76_RS01840
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 BWI76_RS17835
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 BWI76_RS03135
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