GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Phaeobacter inhibens BS107

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA mannose ABC transporter, ATPase component FrcA PGA1_c28040 PGA1_262p00450
frcB mannose ABC transporter, substrate-binding component FrcB PGA1_c28060
frcC mannose ABC transporter, permease component FrcC PGA1_c28050 PGA1_c23080
man-isomerase D-mannose isomerase PGA1_c16670
scrK fructokinase PGA1_c28020
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)
glcV mannose ABC transporter, ATPase component GlcV PGA1_c02740 PGA1_c27320
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component PGA1_c23060 PGA1_c26910
HSERO_RS03645 mannose ABC transporter, permease component PGA1_c23080 PGA1_c28050
manA mannose-6-phosphate isomerase PGA1_65p00290 PGA1_c06550
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 PGA1_c10110 PGA1_c06790
TM1748 mannose ABC transporter, permease component 2 PGA1_c16290 PGA1_c06800
TM1749 mannose ABC transporter, ATPase component 1 PGA1_262p00330 PGA1_262p01010
TM1750 mannose ABC transporter, ATPase component 2 PGA1_262p01000 PGA1_262p00340
TT_C0211 mannose ABC transporter, ATPase component MalK1 PGA1_c16680 PGA1_c07440
TT_C0326 mannose ABC transporter, permease component 2 PGA1_c19480 PGA1_78p00180
TT_C0327 mannose ABC transporter, permease component 1
TT_C0328 mannose ABC transporter, substrate-binding component PGA1_c19500

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