GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Sinorhizobium meliloti 1021

Best path

SM_b21216, SM_b21219, SM_b21220, SM_b21221, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SM_b21216 ABC transporter for D-Glucosamine, ATPase component SM_b21216 SMc04393
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 SM_b21219 SMa0711
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 SM_b21220 SM_b21149
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein SM_b21221
glc-kinase glucosamine kinase SM_b21217 SMc02835
nagB glucosamine 6-phosphate deaminase (isomerizing) SM_b21218 SMc02877
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component SM_b21135 SMa0495
AO353_21715 glucosaminate ABC transporter, permease component 1 SM_b21136 SMc03133
AO353_21720 glucosaminate ABC transporter, permease component 2 SM_b21137 SMc03893
AO353_21725 glucosaminate ABC transporter, ATPase component SM_b21138 SMc02260
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase SMc00110 SMa0564
glucosaminate-lyase glucosaminate ammonia-lyase SMc01224
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 SMc02043 SMc03153
kdgK 2-keto-3-deoxygluconate kinase SMc01531 SM_b21374
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 SMc02878
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) SMc02437
nagK N-acetylglucosamine kinase SMc02875 SMc02880
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) SM_b20232 SMc04136
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) SM_b21105 SMc02871
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
SMc02869 N-acetylglucosamine ABC transporter, ATPase component SMc02869 SMc01499
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 SMc02871 SMc01979
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 SMc02872 SMc02472
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component SMc02873

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