GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Amantichitinum ursilacus IGB-41

Best path

gamP, nagB

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) WG78_RS10305 WG78_RS13865
nagB glucosamine 6-phosphate deaminase (isomerizing) WG78_RS10480 WG78_RS05760
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 WG78_RS08860 WG78_RS15275
AO353_21720 glucosaminate ABC transporter, permease component 2 WG78_RS08860 WG78_RS15275
AO353_21725 glucosaminate ABC transporter, ATPase component WG78_RS16125 WG78_RS16145
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr WG78_RS13860 WG78_RS10305
gdh quinoprotein glucose dehydrogenase
glc-kinase glucosamine kinase
glucosaminate-lyase glucosaminate ammonia-lyase WG78_RS13355 WG78_RS01055
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 WG78_RS07225 WG78_RS19240
kdgK 2-keto-3-deoxygluconate kinase WG78_RS13085 WG78_RS01040
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 WG78_RS09480
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components WG78_RS13865 WG78_RS06315
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components WG78_RS10305 WG78_RS13865
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) WG78_RS10305 WG78_RS13865
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) WG78_RS13860 WG78_RS18545
nagK N-acetylglucosamine kinase WG78_RS08970
nagP N-acetylglucosamine transporter NagP WG78_RS19555
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP WG78_RS10305 WG78_RS13865
nagX transmembrane glucosamine N-acetyltransferase NagX
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) WG78_RS19490 WG78_RS09985
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) WG78_RS07485 WG78_RS09980
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB WG78_RS13865 WG78_RS06315
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC WG78_RS13865 WG78_RS06315
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component WG78_RS08570 WG78_RS08940
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 WG78_RS06135 WG78_RS09980
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 WG78_RS20145 WG78_RS19490
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component WG78_RS08940 WG78_RS07490
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 WG78_RS07485 WG78_RS19495
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 WG78_RS07480 WG78_RS19490
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component WG78_RS07475

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 24 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:

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