GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

nagP, nagK, 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
nagP N-acetylglucosamine transporter NagP CEV31_RS19855
nagK N-acetylglucosamine kinase CEV31_RS13935 CEV31_RS16780
nagA N-acetylglucosamine 6-phosphate deacetylase CEV31_RS16785
nagB glucosamine 6-phosphate deaminase (isomerizing) CEV31_RS02505 CEV31_RS16775
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr CEV31_RS13155
nag3 N-acetylglucosamine transporter nag3/nag4
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) CEV31_RS13155
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) CEV31_RS04205
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) CEV31_RS16740
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) CEV31_RS06770 CEV31_RS07125
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC
SMc02869 N-acetylglucosamine ABC transporter, ATPase component CEV31_RS15275 CEV31_RS07120
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 CEV31_RS07125 CEV31_RS15280
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 CEV31_RS16740
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