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 (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