GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Phaeacidiphilus oryzae TH49

Best path

nagX, crr, ptsB, ptsC, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
nagX transmembrane glucosamine N-acetyltransferase NagX
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr BS73_RS34130
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB BS73_RS24575
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC BS73_RS24565 BS73_RS24570
nagA N-acetylglucosamine 6-phosphate deacetylase BS73_RS17930
nagB glucosamine 6-phosphate deaminase (isomerizing) BS73_RS16650 BS73_RS15815
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 BS73_RS01490 BS73_RS01470
AO353_21720 glucosaminate ABC transporter, permease component 2 BS73_RS15735 BS73_RS01470
AO353_21725 glucosaminate ABC transporter, ATPase component BS73_RS32880 BS73_RS15740
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) BS73_RS24565
gdh quinoprotein glucose dehydrogenase
glc-kinase glucosamine kinase BS73_RS28445 BS73_RS29735
glucosaminate-lyase glucosaminate ammonia-lyase BS73_RS19640 BS73_RS31550
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 BS73_RS13710 BS73_RS31540
kdgK 2-keto-3-deoxygluconate kinase BS73_RS13700 BS73_RS31555
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 BS73_RS24565 BS73_RS24570
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components BS73_RS24565
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) BS73_RS24565 BS73_RS24570
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) BS73_RS34125
nagK N-acetylglucosamine kinase BS73_RS28445 BS73_RS31220
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP BS73_RS24565 BS73_RS24570
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE) BS73_RS20140
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) BS73_RS20145 BS73_RS02465
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG) BS73_RS20150 BS73_RS07030
ngt1 N-acetylglucosamine:H+ symporter Ngt1
SLC2A2 glucosamine transporter SLC2A2 BS73_RS29790
SM_b21216 ABC transporter for D-Glucosamine, ATPase component BS73_RS18100 BS73_RS14235
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 BS73_RS04625 BS73_RS24195
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 BS73_RS24190 BS73_RS33850
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein BS73_RS24185
SMc02869 N-acetylglucosamine ABC transporter, ATPase component BS73_RS18100 BS73_RS07930
SMc02871 N-acetylglucosamine ABC transporter, permease component 2 BS73_RS07030 BS73_RS20150
SMc02872 N-acetylglucosamine ABC transporter, permease component 1 BS73_RS07040 BS73_RS24190
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