GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Acidovorax sp. GW101-3H11

Best path

frcA, frcB, frcC, 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
frcA mannose ABC transporter, ATPase component FrcA Ac3H11_3037 Ac3H11_607
frcB mannose ABC transporter, substrate-binding component FrcB Ac3H11_3035
frcC mannose ABC transporter, permease component FrcC Ac3H11_3036 Ac3H11_1841
man-isomerase D-mannose isomerase Ac3H11_2078
scrK fructokinase Ac3H11_3034 Ac3H11_2936
Alternative steps:
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) Ac3H11_2065
glcV mannose ABC transporter, ATPase component GlcV Ac3H11_2066 Ac3H11_4785
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component Ac3H11_3035
HSERO_RS03640 mannose ABC transporter, ATPase component Ac3H11_2881 Ac3H11_607
HSERO_RS03645 mannose ABC transporter, permease component Ac3H11_3036 Ac3H11_1841
manA mannose-6-phosphate isomerase
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase
manP mannose PTS system, EII-CBA components
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 Ac3H11_4827 Ac3H11_697
TM1748 mannose ABC transporter, permease component 2 Ac3H11_2050 Ac3H11_696
TM1749 mannose ABC transporter, ATPase component 1 Ac3H11_2051 Ac3H11_4825
TM1750 mannose ABC transporter, ATPase component 2 Ac3H11_694 Ac3H11_2052
TT_C0211 mannose ABC transporter, ATPase component MalK1 Ac3H11_4785 Ac3H11_2941
TT_C0326 mannose ABC transporter, permease component 2 Ac3H11_2065
TT_C0327 mannose ABC transporter, permease component 1 Ac3H11_2064
TT_C0328 mannose ABC transporter, substrate-binding component Ac3H11_2062

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 paper from 2022 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