GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Burkholderia phytofirmans PsJN

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA mannose ABC transporter, ATPase component FrcA BPHYT_RS22735 BPHYT_RS30865
frcB mannose ABC transporter, substrate-binding component FrcB BPHYT_RS22745
frcC mannose ABC transporter, permease component FrcC BPHYT_RS22740 BPHYT_RS20745
man-isomerase D-mannose isomerase BPHYT_RS02050
scrK fructokinase BPHYT_RS02045 BPHYT_RS09175
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) BPHYT_RS05035
glcV mannose ABC transporter, ATPase component GlcV BPHYT_RS24660 BPHYT_RS08805
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component BPHYT_RS16065
HSERO_RS03640 mannose ABC transporter, ATPase component BPHYT_RS28215 BPHYT_RS20740
HSERO_RS03645 mannose ABC transporter, permease component BPHYT_RS16055 BPHYT_RS20745
manA mannose-6-phosphate isomerase BPHYT_RS09705 BPHYT_RS03980
manMFS mannose transporter, MFS superfamily BPHYT_RS23445 BPHYT_RS21780
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 BPHYT_RS22050
TM1747 mannose ABC transporter, permease component 1 BPHYT_RS15530 BPHYT_RS22045
TM1748 mannose ABC transporter, permease component 2 BPHYT_RS15525 BPHYT_RS22040
TM1749 mannose ABC transporter, ATPase component 1 BPHYT_RS22035 BPHYT_RS31200
TM1750 mannose ABC transporter, ATPase component 2 BPHYT_RS22030 BPHYT_RS31205
TT_C0211 mannose ABC transporter, ATPase component MalK1 BPHYT_RS35680 BPHYT_RS22760
TT_C0326 mannose ABC transporter, permease component 2 BPHYT_RS05035 BPHYT_RS29180
TT_C0327 mannose ABC transporter, permease component 1
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:

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