GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Ruegeria conchae TW15

Best path

frcA, frcB, frcC, man-isomerase, scrK

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA mannose ABC transporter, ATPase component FrcA G7G_RS0115760 G7G_RS0103335
frcB mannose ABC transporter, substrate-binding component FrcB G7G_RS0115750
frcC mannose ABC transporter, permease component FrcC G7G_RS0115755 G7G_RS0100410
man-isomerase D-mannose isomerase G7G_RS0111755
scrK fructokinase G7G_RS0111340 G7G_RS0119975
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 G7G_RS0114935 G7G_RS0115525
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component G7G_RS0100415 G7G_RS0100435
HSERO_RS03645 mannose ABC transporter, permease component G7G_RS0100410 G7G_RS0115755
manA mannose-6-phosphate isomerase G7G_RS0111220 G7G_RS0105430
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 G7G_RS0111195
TM1747 mannose ABC transporter, permease component 1 G7G_RS0111200 G7G_RS0117775
TM1748 mannose ABC transporter, permease component 2 G7G_RS0111205 G7G_RS0117780
TM1749 mannose ABC transporter, ATPase component 1 G7G_RS0120955 G7G_RS0117765
TM1750 mannose ABC transporter, ATPase component 2 G7G_RS0111210 G7G_RS0120960
TT_C0211 mannose ABC transporter, ATPase component MalK1 G7G_RS0110555 G7G_RS0121175
TT_C0326 mannose ABC transporter, permease component 2 G7G_RS0103680 G7G_RS0117195
TT_C0327 mannose ABC transporter, permease component 1 G7G_RS0103675
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 24 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