GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Marinomonas arctica 328

Best path

nagX, SMc02869, SMc02872, SMc02871, SMc02873, nagK, nagA, 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
nagX transmembrane glucosamine N-acetyltransferase NagX
SMc02869 N-acetylglucosamine ABC transporter, ATPase component DK187_RS16415 DK187_RS02530
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 DK187_RS20425
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 DK187_RS20420 DK187_RS02525
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component DK187_RS20430
nagK N-acetylglucosamine kinase DK187_RS20440 DK187_RS01540
nagA N-acetylglucosamine 6-phosphate deacetylase DK187_RS20445
nagB glucosamine 6-phosphate deaminase (isomerizing) DK187_RS20435 DK187_RS09415
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 DK187_RS16320 DK187_RS13625
AO353_21720 glucosaminate ABC transporter, permease component 2 DK187_RS16320 DK187_RS20500
AO353_21725 glucosaminate ABC transporter, ATPase component DK187_RS13615 DK187_RS20495
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase DK187_RS01750 DK187_RS10780
glc-kinase glucosamine kinase DK187_RS20440 DK187_RS01540
glucosaminate-lyase glucosaminate ammonia-lyase DK187_RS05240 DK187_RS11230
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 DK187_RS01530 DK187_RS11900
kdgK 2-keto-3-deoxygluconate kinase DK187_RS16375
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) DK187_RS15085
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) DK187_RS09455
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) DK187_RS20420 DK187_RS11925
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 DK187_RS03285 DK187_RS17255
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 DK187_RS02525
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 DK187_RS02520 DK187_RS13510
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 24 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:

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