GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

mtlG, mtlF, mtlE, mtlK, 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.

36 steps (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mtlG mannose ABC transporter, permease component 1 (MtlG) Pf1N1B4_4848 Pf1N1B4_5114
mtlF mannose ABC transporter, permease component 2 (MtlF) Pf1N1B4_4849 Pf1N1B4_5113
mtlE mannose ABC transporter, substrate-binding component MtlE Pf1N1B4_4850 Pf1N1B4_5038
mtlK mannose ABC transporter, ATPase component MtlK Pf1N1B4_4847 Pf1N1B4_5115
man-isomerase D-mannose isomerase Pf1N1B4_597
scrK fructokinase Pf1N1B4_4844 Pf1N1B4_4765
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA Pf1N1B4_4286 Pf1N1B4_6034
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC Pf1N1B4_4287 Pf1N1B4_409
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) Pf1N1B4_594
glcV mannose ABC transporter, ATPase component GlcV Pf1N1B4_2538 Pf1N1B4_4352
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component Pf1N1B4_4286 Pf1N1B4_410
HSERO_RS03645 mannose ABC transporter, permease component Pf1N1B4_4287 Pf1N1B4_6033
manA mannose-6-phosphate isomerase Pf1N1B4_993 Pf1N1B4_1964
manMFS mannose transporter, MFS superfamily Pf1N1B4_397 Pf1N1B4_3380
mannokinase D-mannose kinase
manP mannose PTS system, EII-CBA components Pf1N1B4_1144
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 Pf1N1B4_5627 Pf1N1B4_5102
TM1748 mannose ABC transporter, permease component 2 Pf1N1B4_1125 Pf1N1B4_5103
TM1749 mannose ABC transporter, ATPase component 1 Pf1N1B4_5104 Pf1N1B4_1126
TM1750 mannose ABC transporter, ATPase component 2 Pf1N1B4_1127 Pf1N1B4_5105
TT_C0211 mannose ABC transporter, ATPase component MalK1 Pf1N1B4_5115 Pf1N1B4_593
TT_C0326 mannose ABC transporter, permease component 2 Pf1N1B4_594 Pf1N1B4_5114
TT_C0327 mannose ABC transporter, permease component 1 Pf1N1B4_595
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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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