GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Sinorhizobium fredii NGR234

Best path

SM_b21216, SM_b21219, SM_b21220, SM_b21221, glc-kinase, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SM_b21216 ABC transporter for D-Glucosamine, ATPase component NGR_RS05625 NGR_RS27670
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 NGR_RS05640 NGR_RS08910
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 NGR_RS05645 NGR_RS06235
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein NGR_RS05650
glc-kinase glucosamine kinase NGR_RS05630 NGR_RS28545
nagB glucosamine 6-phosphate deaminase (isomerizing) NGR_RS05635 NGR_RS28770
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component NGR_RS05595
AO353_21715 glucosaminate ABC transporter, permease component 1 NGR_RS05600 NGR_RS10550
AO353_21720 glucosaminate ABC transporter, permease component 2 NGR_RS05605 NGR_RS27540
AO353_21725 glucosaminate ABC transporter, ATPase component NGR_RS05610 NGR_RS00810
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr
gamP glucosamine PTS system, EII-CBA components (GamP/NagE)
gdh quinoprotein glucose dehydrogenase NGR_RS15020 NGR_RS22565
glucosaminate-lyase glucosaminate ammonia-lyase NGR_RS02765 NGR_RS19070
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 NGR_RS25805 NGR_RS13545
kdgK 2-keto-3-deoxygluconate kinase NGR_RS23025 NGR_RS24125
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 NGR_RS28775
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) NGR_RS02015 NGR_RS24430
nagK N-acetylglucosamine kinase NGR_RS28760 NGR_RS28785
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) NGR_RS08650 NGR_RS09950
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) NGR_RS28740 NGR_RS08910
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 NGR_RS28730 NGR_RS23510
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 NGR_RS28740 NGR_RS23885
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 NGR_RS28745 NGR_RS05645
SMc02873 N-acetylglucosamine ABC transporter, substrate-binding component NGR_RS28750

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