GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Pseudomonas simiae WCS417

Best path

gdh, AO353_21715, AO353_21720, AO353_21725, AO353_21710, glucosaminate-lyase, kdgK, kdgA

Also see fitness data for the top candidates

Rules

Overview: The canonical pathway for glucosamine utilization involves glucosamine 6-phosphate as an intermediate, as in N-acetylglucosamine utilization (link). GapMind also includes two other pathways: an oxidative pathway via glucosaminate ammonia-lyase, and a transmembrane transacetylase (NagX) pathway.

40 steps (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gdh quinoprotein glucose dehydrogenase PS417_05300 PS417_10960
AO353_21715 glucosaminate ABC transporter, permease component 1 PS417_12100 PS417_01015
AO353_21720 glucosaminate ABC transporter, permease component 2 PS417_12105 PS417_01020
AO353_21725 glucosaminate ABC transporter, ATPase component PS417_12110 PS417_18120
AO353_21710 glucosaminate ABC transporter, substrate-binding component PS417_12095
glucosaminate-lyase glucosaminate ammonia-lyase PS417_12125 PS417_23515
kdgK 2-keto-3-deoxygluconate kinase PS417_12130 PS417_12565
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 PS417_22100 PS417_00160
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr PS417_22995 PS417_23035
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) PS417_23000
glc-kinase glucosamine kinase PS417_22685
manX glucosamine PTS system, EII-AB component ManX
manY glucosamine PTS system, EII-C component ManY
manZ glucosamine PTS system, EII-D component ManZ
nag3 N-acetylglucosamine transporter nag3/nag4
nagA N-acetylglucosamine 6-phosphate deacetylase PS417_22985
nagB glucosamine 6-phosphate deaminase (isomerizing) PS417_22990 PS417_28445
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components PS417_23000
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components PS417_23000
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) PS417_23000 PS417_22995
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) PS417_22995 PS417_23035
nagK N-acetylglucosamine kinase PS417_22685
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP PS417_23000
nagX transmembrane glucosamine N-acetyltransferase NagX
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) PS417_22135
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB PS417_23000
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC PS417_23000
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component PS417_22130 PS417_12700
SM_b21219 ABC transporter for D-Glucosamine, permease component 1
SM_b21220 ABC transporter for D-Glucosamine, permease component 2
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component PS417_12700 PS417_22130
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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