GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Escherichia coli BW25113

Best path

manX, manY, manZ, manA

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manX mannose PTS system, EII-AB component ManX/ManL b1817
manY mannose PTS system, EII-C component ManY/ManM b1818
manZ mannose PTS system, EII-D component ManZ/ManN b1819 b3140
manA mannose-6-phosphate isomerase b1613 b2049
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA b4485 b3749
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC b3750 b2148
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 b0262 b4035
gluP mannose:Na+ symporter b2801
HSERO_RS03635 mannose ABC transporter, substrate-binding component b3751
HSERO_RS03640 mannose ABC transporter, ATPase component b3749 b1900
HSERO_RS03645 mannose ABC transporter, permease component b3750 b2546
man-isomerase D-mannose isomerase b3880
manMFS mannose transporter, MFS superfamily b4356 b3691
mannokinase D-mannose kinase b0394 b1119
manP mannose PTS system, EII-CBA components b2167 b3899
MST1 mannose:H+ symporter
scrK fructokinase b0394 b1119
STP6 mannose:H+ symporter b2943
TM1746 mannose ABC transporter, substrate-binding component b1243
TM1747 mannose ABC transporter, permease component 1 b1244 b0831
TM1748 mannose ABC transporter, permease component 2 b0832 b1245
TM1749 mannose ABC transporter, ATPase component 1 b1246 b3541
TM1750 mannose ABC transporter, ATPase component 2 b3540 b1247
TT_C0211 mannose ABC transporter, ATPase component MalK1 b4035 b3450
TT_C0326 mannose ABC transporter, permease component 2 b4032
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 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, 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