GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Azospirillum brasilense Sp245

Best path

SLC2A2, glc-kinase, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SLC2A2 glucosamine transporter SLC2A2
glc-kinase glucosamine kinase AZOBR_RS05405 AZOBR_RS27950
nagB glucosamine 6-phosphate deaminase (isomerizing) AZOBR_RS25530 AZOBR_RS09675
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component AZOBR_RS10265 AZOBR_RS15685
AO353_21715 glucosaminate ABC transporter, permease component 1 AZOBR_RS15675 AZOBR_RS27070
AO353_21720 glucosaminate ABC transporter, permease component 2 AZOBR_RS23520 AZOBR_RS29610
AO353_21725 glucosaminate ABC transporter, ATPase component AZOBR_RS00690 AZOBR_RS26405
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase AZOBR_RS31355
glucosaminate-lyase glucosaminate ammonia-lyase AZOBR_RS12935 AZOBR_RS26420
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 AZOBR_RS29850 AZOBR_RS22730
kdgK 2-keto-3-deoxygluconate kinase AZOBR_RS29860
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 AZOBR_RS11675
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) AZOBR_RS32325 AZOBR_RS30470
nagK N-acetylglucosamine kinase AZOBR_RS11685 AZOBR_RS05405
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP
nagX transmembrane glucosamine N-acetyltransferase NagX
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) AZOBR_RS25585
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) AZOBR_RS25590 AZOBR_RS27985
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
SM_b21216 ABC transporter for D-Glucosamine, ATPase component AZOBR_RS00060 AZOBR_RS27980
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 AZOBR_RS27985 AZOBR_RS25590
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 AZOBR_RS25585 AZOBR_RS18175
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component AZOBR_RS25595 AZOBR_RS00060
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 AZOBR_RS18180 AZOBR_RS27985
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 (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 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