GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Photobacterium jeanii R-40508

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) A3K86_RS02285 A3K86_RS02900
nagB glucosamine 6-phosphate deaminase (isomerizing) A3K86_RS06400 A3K86_RS16395
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 A3K86_RS21195 A3K86_RS17300
AO353_21720 glucosaminate ABC transporter, permease component 2 A3K86_RS21195 A3K86_RS01695
AO353_21725 glucosaminate ABC transporter, ATPase component A3K86_RS13000 A3K86_RS01690
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr A3K86_RS12910
gdh quinoprotein glucose dehydrogenase
glc-kinase glucosamine kinase A3K86_RS10945
glucosaminate-lyase glucosaminate ammonia-lyase A3K86_RS05680 A3K86_RS16195
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 A3K86_RS14285 A3K86_RS16310
kdgK 2-keto-3-deoxygluconate kinase A3K86_RS14280 A3K86_RS16315
manX glucosamine PTS system, EII-AB component ManX
manY glucosamine PTS system, EII-C component ManY
manZ glucosamine PTS system, EII-D component ManZ A3K86_RS16380
nag3 N-acetylglucosamine transporter nag3/nag4
nagA N-acetylglucosamine 6-phosphate deacetylase A3K86_RS06405 A3K86_RS21450
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components A3K86_RS02285 A3K86_RS02900
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components A3K86_RS02285 A3K86_RS06395
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) A3K86_RS02900 A3K86_RS05470
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) A3K86_RS12915 A3K86_RS11265
nagK N-acetylglucosamine kinase A3K86_RS03930 A3K86_RS10945
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP A3K86_RS02285 A3K86_RS14160
nagX transmembrane glucosamine N-acetyltransferase NagX
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) A3K86_RS19335
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG)
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB A3K86_RS06395 A3K86_RS02285
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC A3K86_RS02285 A3K86_RS02900
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component A3K86_RS19360 A3K86_RS19475
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 A3K86_RS19490
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 A3K86_RS19335
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component A3K86_RS19475 A3K86_RS19360
SMc02871 N-acetylglucosamine ABC transporter, permease component 2
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 A3K86_RS19335
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 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