GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism in Chromobacterium vaccinii MWU205

Best path

nagF, nagEcb, nagA, nagB

Rules

Overview: N-acetylglucosamine utilization in GapMind is based on MetaCyc pathways N-acetylglucosamine degradation I (link) and pathway II (link). These pathways differ in whether uptake and phosphorylation are performed by a PTS system or performed separately by a transporter and a kinase.

21 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) VL52_RS06575 VL52_RS01610
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components VL52_RS06570 VL52_RS01615
nagA N-acetylglucosamine 6-phosphate deacetylase VL52_RS06585
nagB glucosamine 6-phosphate deaminase (isomerizing) VL52_RS06580 VL52_RS20250
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr VL52_RS01610 VL52_RS06575
nag3 N-acetylglucosamine transporter nag3/nag4
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components VL52_RS06570 VL52_RS01615
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) VL52_RS01615 VL52_RS06570
nagK N-acetylglucosamine kinase VL52_RS05495 VL52_RS08430
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP VL52_RS06570 VL52_RS01615
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) VL52_RS04905 VL52_RS08420
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 VL52_RS06570 VL52_RS01615
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC VL52_RS06570 VL52_RS01615
SMc02869 N-acetylglucosamine ABC transporter, ATPase component VL52_RS04920 VL52_RS12740
SMc02871 N-acetylglucosamine ABC transporter, permease component 2
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 VL52_RS04905 VL52_RS08420
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