GapMind for catabolism of small carbon sources

 

N-acetyl-D-glucosamine catabolism in Collinsella tanakaei YIT 12063

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components
nagA N-acetylglucosamine 6-phosphate deacetylase HMPREF9452_RS03865
nagB glucosamine 6-phosphate deaminase (isomerizing) HMPREF9452_RS06260 HMPREF9452_RS03870
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr HMPREF9452_RS02285 HMPREF9452_RS06255
nag3 N-acetylglucosamine transporter nag3/nag4
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components HMPREF9452_RS09360
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) HMPREF9452_RS09360 HMPREF9452_RS02285
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) HMPREF9452_RS01785
nagK N-acetylglucosamine kinase HMPREF9452_RS05275
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP HMPREF9452_RS09360
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 HMPREF9452_RS02680 HMPREF9452_RS05760
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC HMPREF9452_RS09360
SMc02869 N-acetylglucosamine ABC transporter, ATPase component HMPREF9452_RS08560 HMPREF9452_RS09060
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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