GapMind for catabolism of small carbon sources

 

Definition of D-mannose catabolism

As rules and steps, or see full text

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.

Steps

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

manP: mannose PTS system, EII-CBA components

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

TT_C0211: mannose ABC transporter, ATPase component MalK1

TT_C0327: mannose ABC transporter, permease component 1

TT_C0326: mannose ABC transporter, permease component 2

TT_C0328: mannose ABC transporter, substrate-binding component

TM1746: mannose ABC transporter, substrate-binding component

TM1747: mannose ABC transporter, permease component 1

TM1748: mannose ABC transporter, permease component 2

TM1749: mannose ABC transporter, ATPase component 1

TM1750: mannose ABC transporter, ATPase component 2

frcA: mannose ABC transporter, ATPase component FrcA

frcB: mannose ABC transporter, substrate-binding component FrcB

frcC: mannose ABC transporter, permease component FrcC

HSERO_RS03635: mannose ABC transporter, substrate-binding component

HSERO_RS03640: mannose ABC transporter, ATPase component

HSERO_RS03645: mannose ABC transporter, permease component

STP6: mannose:H+ symporter

gluP: mannose:Na+ symporter

glcP: mannose:H+ symporter

MST1: mannose:H+ symporter

manMFS: mannose transporter, MFS superfamily

manA: mannose-6-phosphate isomerase

man-isomerase: D-mannose isomerase

mannokinase: D-mannose kinase

scrK: fructokinase

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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, 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