GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Belnapia rosea CPCC 100156

Best path

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

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gdh quinoprotein glucose dehydrogenase BLR02_RS21990
AO353_21715 glucosaminate ABC transporter, permease component 1 BLR02_RS02410 BLR02_RS19470
AO353_21720 glucosaminate ABC transporter, permease component 2 BLR02_RS10410 BLR02_RS19470
AO353_21725 glucosaminate ABC transporter, ATPase component BLR02_RS10420 BLR02_RS02400
AO353_21710 glucosaminate ABC transporter, substrate-binding component
glucosaminate-lyase glucosaminate ammonia-lyase BLR02_RS18980
kdgK 2-keto-3-deoxygluconate kinase BLR02_RS17285 BLR02_RS22555
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 BLR02_RS16045 BLR02_RS17280
Alternative steps:
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
glc-kinase glucosamine kinase BLR02_RS12205 BLR02_RS01805
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
nagB glucosamine 6-phosphate deaminase (isomerizing) BLR02_RS07310
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) BLR02_RS10210 BLR02_RS24985
nagK N-acetylglucosamine kinase BLR02_RS12205 BLR02_RS06040
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) BLR02_RS22755
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
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component BLR02_RS07875 BLR02_RS15665
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 BLR02_RS15660 BLR02_RS07860
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 BLR02_RS27605 BLR02_RS07865
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component BLR02_RS07875 BLR02_RS00310
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 BLR02_RS22750
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 BLR02_RS07865
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