D-glucosamine (chitosamine) catabolism in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

D-glucosamine (chitosamine) catabolism in Herbaspirillum seropedicae SmR1

Best path

nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, nagB

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.

all:

gdh, glucosaminate-transport, glucosaminate-lyase, kdgK and kdgA
or glucosamine-transport, glc-kinase and nagB
or glucosamine-PTS and nagB
or nagX and NAG-utilization
Comment: The glucosaminate pathway begins with the periplasmic glucose dehydrogenase (gdh; PMID:1849886). (It is not clear if gdh forms glucosaminate directly or forms a lactone intermediate; the latter seems more likely but has not been demonstrated, nor has a lactonase been identified by genetics; or the lactone might hydrolyze spontaneously.) Glucosaminate is then taken up and converted to 2-keto-3-deoxygluconate by an ammonia-lyase (EC 4.3.1.9) and phosphorylated (by kdgK) to enter the Entner-Doudoroff pathway. (No phenotypes for kdgK were identified in the genetic data, but this step could be genetically redundant. It is also reported that the glucosaminate dehydratase has some aldolase activity, producing glyceraldehye and pyruvate (PMID:7766176).) Alternatively, glucosamine kinase forms glucosamine-6-phosphate, which can be converted by nagB (glucosamine 6-phosphate deaminase (isomerizing)) to fructose-6-phosphate. Glucosamine 6-phosphate can also be formed by PTS systems. Alternatively, the transmembrane transacetylase (NagX) route involves conversion in the periplasm to N-acetylglucosamine.

NAG-utilization:

NAG-PTS, nagA and nagB
or NAG-transport, nagK, nagA and nagB
Comment: Both pathways involve N-acetylglucosamine 6-phosphate, followed by deacetylase nagA and the isomerizing deaminase nagB, which produces fructose 6-phosphate, a central metabolic intermediate.

NAG-transport:

SMc02869, SMc02872, SMc02871 and SMc02873
or ngcE, ngcF and ngcG
or nagP
or nag3
or ngt1
Comment: Transporters were identified using: query: transporter:N-acetylglucosamine:N-ACETYL-D-GLUCOSAMINE:CPD-12541

NAG-PTS:

nagEcba
or nagF and nagEcb
or crr, ptsB and ptsC
or nagEIIA and nagPcb
Comment: PTS systems form N-acetylglucosamine 6-phosphate

glucosamine-PTS:

gamP
or manX, manY and manZ
Comment: PTS systems (forming glucosamine-6-phosphate)

glucosaminate-transport: AO353_21715, AO353_21720, AO353_21725 and AO353_21710
glucosamine-transport:

SM_b21216, SM_b21219, SM_b21220 and SM_b21221
or SLC2A2
Comment: Transporters and PTS systems were identified using query: transporter:glucosamine:D-glucosamine:CPD-12538:CPD-12539

40 steps (19 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
nagX	transmembrane glucosamine N-acetyltransferase NagX
SMc02869	N-acetylglucosamine ABC transporter, ATPase component	HSERO_RS16715	HSERO_RS22750
SMc02872	N-acetylglucosamine ABC transporter, permease component 1	HSERO_RS22740
SMc02871	N-acetylglucosamine ABC transporter, permease component 2	HSERO_RS22745	HSERO_RS01335
SMc02873	N-acetylglucosamine ABC transporter, substrate-binding component	HSERO_RS22735
nagK	N-acetylglucosamine kinase	HSERO_RS17870	HSERO_RS22755
nagA	N-acetylglucosamine 6-phosphate deacetylase	HSERO_RS22760
nagB	glucosamine 6-phosphate deaminase (isomerizing)	HSERO_RS22765	HSERO_RS22125
Alternative steps:
AO353_21710	glucosaminate ABC transporter, substrate-binding component
AO353_21715	glucosaminate ABC transporter, permease component 1	HSERO_RS23035	HSERO_RS17545
AO353_21720	glucosaminate ABC transporter, permease component 2	HSERO_RS10770	HSERO_RS11445
AO353_21725	glucosaminate ABC transporter, ATPase component	HSERO_RS00320	HSERO_RS19345
crr	N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP	glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh	quinoprotein glucose dehydrogenase
glc-kinase	glucosamine kinase	HSERO_RS17870	HSERO_RS22755
glucosaminate-lyase	glucosaminate ammonia-lyase	HSERO_RS08720	HSERO_RS09495
kdgA	2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14	HSERO_RS05525	HSERO_RS05155
kdgK	2-keto-3-deoxygluconate kinase	HSERO_RS08715	HSERO_RS07545
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
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)
nagF	N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF)	HSERO_RS00450
nagP	N-acetylglucosamine transporter NagP
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)
ngcG	N-acetylglucosamine ABC transporter, permease component 2 (NgcG)	HSERO_RS22745	HSERO_RS01335
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
SLC2A2	glucosamine transporter SLC2A2
SM_b21216	ABC transporter for D-Glucosamine, ATPase component	HSERO_RS16715	HSERO_RS18940
SM_b21219	ABC transporter for D-Glucosamine, permease component 1	HSERO_RS16730	HSERO_RS02200
SM_b21220	ABC transporter for D-Glucosamine, permease component 2	HSERO_RS16725	HSERO_RS15495
SM_b21221	ABC transporter for D-Glucosamine, substrate-binding protein

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources