GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

manMFS, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manMFS mannose transporter, MFS superfamily AO356_28540 AO356_07175
man-isomerase D-mannose isomerase AO356_05200
scrK fructokinase AO356_00035 AO356_27700
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA AO356_23205 AO356_28510
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC AO356_23210 AO356_20255
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 AO356_14385 AO356_13165
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component AO356_23200
HSERO_RS03640 mannose ABC transporter, ATPase component AO356_23205 AO356_20250
HSERO_RS03645 mannose ABC transporter, permease component AO356_23210 AO356_00960
manA mannose-6-phosphate isomerase AO356_17260 AO356_11830
mannokinase D-mannose kinase
manP mannose PTS system, EII-CBA components AO356_07325
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 AO356_29375 AO356_07705
TM1748 mannose ABC transporter, permease component 2 AO356_06860 AO356_07265
TM1749 mannose ABC transporter, ATPase component 1 AO356_07715 AO356_07270
TM1750 mannose ABC transporter, ATPase component 2 AO356_29390 AO356_07275
TT_C0211 mannose ABC transporter, ATPase component MalK1 AO356_28585 AO356_05180
TT_C0326 mannose ABC transporter, permease component 2 AO356_05185 AO356_28580
TT_C0327 mannose ABC transporter, permease component 1 AO356_05190
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 (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 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