GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Brucella inopinata BO1

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 (22 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 BIBO1_RS17490 BIBO1_RS16200
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 BIBO1_RS17475
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 BIBO1_RS17480 BIBO1_RS16195
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component BIBO1_RS17470
nagK N-acetylglucosamine kinase BIBO1_RS17465 BIBO1_RS15200
nagA N-acetylglucosamine 6-phosphate deacetylase BIBO1_RS18780
nagB glucosamine 6-phosphate deaminase (isomerizing) BIBO1_RS18785 BIBO1_RS17675
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component BIBO1_RS17110 BIBO1_RS09035
AO353_21715 glucosaminate ABC transporter, permease component 1 BIBO1_RS19985 BIBO1_RS17105
AO353_21720 glucosaminate ABC transporter, permease component 2 BIBO1_RS17105 BIBO1_RS14880
AO353_21725 glucosaminate ABC transporter, ATPase component BIBO1_RS14870 BIBO1_RS07180
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 BIBO1_RS19405 BIBO1_RS17465
glucosaminate-lyase glucosaminate ammonia-lyase BIBO1_RS11015
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 BIBO1_RS15530 BIBO1_RS18915
kdgK 2-keto-3-deoxygluconate kinase BIBO1_RS08880 BIBO1_RS16980
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) BIBO1_RS12560
nagP N-acetylglucosamine transporter NagP BIBO1_RS15725
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) BIBO1_RS12770 BIBO1_RS17480
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 BIBO1_RS12775 BIBO1_RS17945
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 BIBO1_RS12770 BIBO1_RS16195
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 BIBO1_RS16190 BIBO1_RS17960
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein BIBO1_RS12760

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