GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism in Alkalihalobacterium alkalinitrilicum DSM 22532

Best path

nagEIIA, nagPcb, 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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) BK574_RS22665 BK574_RS10715
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP BK574_RS22665
nagA N-acetylglucosamine 6-phosphate deacetylase BK574_RS14455
nagB glucosamine 6-phosphate deaminase (isomerizing) BK574_RS14450 BK574_RS17170
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr BK574_RS22665 BK574_RS10715
nag3 N-acetylglucosamine transporter nag3/nag4
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components BK574_RS22665
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components BK574_RS22665
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) BK574_RS22675
nagK N-acetylglucosamine kinase BK574_RS12335 BK574_RS14475
nagP N-acetylglucosamine transporter NagP
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF)
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 BK574_RS22665
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC BK574_RS22665
SMc02869 N-acetylglucosamine ABC transporter, ATPase component BK574_RS17060 BK574_RS01510
SMc02871 N-acetylglucosamine ABC transporter, permease component 2
SMc02872 N-acetylglucosamine ABC transporter, permease component 1
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 Apr 09 2024. 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