GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism in Photobacterium jeanii R-40508

Best path

nagEcba, 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
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components A3K86_RS02285 A3K86_RS06395
nagA N-acetylglucosamine 6-phosphate deacetylase A3K86_RS06405 A3K86_RS21450
nagB glucosamine 6-phosphate deaminase (isomerizing) A3K86_RS06400 A3K86_RS16395
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr A3K86_RS12910
nag3 N-acetylglucosamine transporter nag3/nag4
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components A3K86_RS02285 A3K86_RS02900
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
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
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