GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Paraburkholderia phymatum STM815

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) BPHY_RS01460
nagB glucosamine 6-phosphate deaminase (isomerizing) BPHY_RS01450 BPHY_RS14725
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component BPHY_RS33245
AO353_21715 glucosaminate ABC transporter, permease component 1 BPHY_RS05855 BPHY_RS33250
AO353_21720 glucosaminate ABC transporter, permease component 2 BPHY_RS27410 BPHY_RS07800
AO353_21725 glucosaminate ABC transporter, ATPase component BPHY_RS25605 BPHY_RS30385
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr BPHY_RS01455
gdh quinoprotein glucose dehydrogenase BPHY_RS27845
glc-kinase glucosamine kinase BPHY_RS03130 BPHY_RS15200
glucosaminate-lyase glucosaminate ammonia-lyase BPHY_RS01810 BPHY_RS03175
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 BPHY_RS13275 BPHY_RS13085
kdgK 2-keto-3-deoxygluconate kinase BPHY_RS04935 BPHY_RS06360
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 BPHY_RS01445
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components BPHY_RS01460
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components BPHY_RS01460
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) BPHY_RS01460 BPHY_RS01455
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) BPHY_RS01455 BPHY_RS01300
nagK N-acetylglucosamine kinase BPHY_RS15200 BPHY_RS03130
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP BPHY_RS01460
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) BPHY_RS11935 BPHY_RS36880
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB BPHY_RS01460
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC BPHY_RS01460
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component BPHY_RS03160 BPHY_RS20430
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 BPHY_RS20450 BPHY_RS02470
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 BPHY_RS20445 BPHY_RS31700
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component BPHY_RS02480 BPHY_RS13785
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 BPHY_RS11935
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