GapMind for catabolism of small carbon sources

 

D-glucosamine (chitosamine) catabolism in Tatumella morbirosei LMG 23360

Best path

manX, manY, manZ, 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
manX glucosamine PTS system, EII-AB component ManX HA49_RS13125
manY glucosamine PTS system, EII-C component ManY HA49_RS13130
manZ glucosamine PTS system, EII-D component ManZ HA49_RS13135
nagB glucosamine 6-phosphate deaminase (isomerizing) HA49_RS15330 HA49_RS18655
Alternative steps:
AO353_21710 glucosaminate ABC transporter, substrate-binding component
AO353_21715 glucosaminate ABC transporter, permease component 1 HA49_RS00170 HA49_RS06600
AO353_21720 glucosaminate ABC transporter, permease component 2 HA49_RS06240 HA49_RS06600
AO353_21725 glucosaminate ABC transporter, ATPase component HA49_RS09820 HA49_RS12345
crr N-acetylglucosamine phosphotransferase system, EII-A component Crr HA49_RS15945 HA49_RS15335
gamP glucosamine PTS system, EII-CBA components (GamP/NagE) HA49_RS15335
gdh quinoprotein glucose dehydrogenase HA49_RS16290 HA49_RS17695
glc-kinase glucosamine kinase HA49_RS08260
glucosaminate-lyase glucosaminate ammonia-lyase HA49_RS01535 HA49_RS07300
kdgA 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 HA49_RS01090
kdgK 2-keto-3-deoxygluconate kinase
nag3 N-acetylglucosamine transporter nag3/nag4
nagA N-acetylglucosamine 6-phosphate deacetylase HA49_RS15325
nagEcb N-acetylglucosamine phosphotransferase system, EII-CB components HA49_RS15335
nagEcba N-acetylglucosamine phosphotransferase system, EII-CBA components HA49_RS15335
nagEIIA N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) HA49_RS15335 HA49_RS08410
nagF N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) HA49_RS08405 HA49_RS06180
nagK N-acetylglucosamine kinase HA49_RS03535 HA49_RS08260
nagP N-acetylglucosamine transporter NagP
nagPcb N-acetylglucosamine phosphotransferase system, EII-CB component NagP HA49_RS15335
nagX transmembrane glucosamine N-acetyltransferase NagX
ngcE N-acetylglucosamine ABC transporter, substrate-binding component (NgcE)
ngcF N-acetylglucosamine ABC transporter, permease component 1 (NgcF) HA49_RS03675
ngcG N-acetylglucosamine ABC transporter, permease component 2 (NgcG)
ngt1 N-acetylglucosamine:H+ symporter Ngt1
ptsB N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB HA49_RS15335
ptsC N-acetylglucosamine phosphotransferase system, EII-C component PtsC HA49_RS15335
SLC2A2 glucosamine transporter SLC2A2
SM_b21216 ABC transporter for D-Glucosamine, ATPase component HA49_RS19415 HA49_RS11785
SM_b21219 ABC transporter for D-Glucosamine, permease component 1 HA49_RS11805
SM_b21220 ABC transporter for D-Glucosamine, permease component 2 HA49_RS03675
SM_b21221 ABC transporter for D-Glucosamine, substrate-binding protein
SMc02869 N-acetylglucosamine ABC transporter, ATPase component HA49_RS11785 HA49_RS19415
SMc02871 N-acetylglucosamine ABC transporter, permease component 2
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 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