GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Alkalihalobacterium alkalinitrilicum DSM 22532

Best path

gamP, nagB

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) BK574_RS22665
nagB glucosamine 6-phosphate deaminase (isomerizing) BK574_RS14450 BK574_RS17170
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 BK574_RS18740 BK574_RS01585
AO353_21720 glucosaminate ABC transporter, permease component 2 BK574_RS01585 BK574_RS11420
AO353_21725 glucosaminate ABC transporter, ATPase component BK574_RS11415 BK574_RS18745
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr BK574_RS22665 BK574_RS10715
gdh quinoprotein glucose dehydrogenase
glc-kinase glucosamine kinase BK574_RS12335 BK574_RS14475
glucosaminate-lyase glucosaminate ammonia-lyase BK574_RS20735 BK574_RS15105
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 BK574_RS15640 BK574_RS09410
kdgK 2-keto-3-deoxygluconate kinase BK574_RS15635 BK574_RS02545
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 BK574_RS14455
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components BK574_RS22665
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components BK574_RS22665
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) BK574_RS22665 BK574_RS10715
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) BK574_RS22675
nagK N-acetylglucosamine kinase BK574_RS12335 BK574_RS14475
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP BK574_RS22665
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)
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB BK574_RS22665
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC BK574_RS22665
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component BK574_RS17060 BK574_RS01510
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 BK574_RS17060 BK574_RS01510
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 Apr 09 2024. 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:

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