GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

gluP, man-isomerase, scrK

Also see fitness data for the top candidates

Rules

Overview: Mannose utilization in GapMind is based on MetaCyc pathways D-mannose degradation I via a PTS system (link), pathway II via mannose kinase (link), or conversion to fructose by mannose isomerase.

32 steps (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gluP mannose:Na+ symporter AO353_25100
man-isomerase D-mannose isomerase AO353_03400
scrK fructokinase AO353_25910 AO353_25105
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA AO353_21385 AO353_20820
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC AO353_21390
glcP mannose:H+ symporter
glcS mannose ABC transporter, substrate-binding component GlcS
glcT mannose ABC transporter, permease component 1 (GlcT)
glcU mannose ABC transporter, permease component 2 (GlcU)
glcV mannose ABC transporter, ATPase component GlcV AO353_07265 AO353_29310
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component AO353_21385 AO353_20820
HSERO_RS03645 mannose ABC transporter, permease component AO353_21390 AO353_20825
manA mannose-6-phosphate isomerase AO353_04735 AO353_02025
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase
manP mannose PTS system, EII-CBA components AO353_05475
manX mannose PTS system, EII-AB component ManX/ManL
manY mannose PTS system, EII-C component ManY/ManM
manZ mannose PTS system, EII-D component ManZ/ManN
MST1 mannose:H+ symporter
STP6 mannose:H+ symporter
TM1746 mannose ABC transporter, substrate-binding component
TM1747 mannose ABC transporter, permease component 1 AO353_21795 AO353_21870
TM1748 mannose ABC transporter, permease component 2 AO353_05400 AO353_21865
TM1749 mannose ABC transporter, ATPase component 1 AO353_21860 AO353_05405
TM1750 mannose ABC transporter, ATPase component 2 AO353_05410 AO353_21855
TT_C0211 mannose ABC transporter, ATPase component MalK1 AO353_25130 AO353_03380
TT_C0326 mannose ABC transporter, permease component 2 AO353_03385 AO353_25125
TT_C0327 mannose ABC transporter, permease component 1 AO353_03390
TT_C0328 mannose 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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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