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.

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.

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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, the preprint on GapMind for carbon sources, 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